Starting phenix.real_space_refine on Mon Mar 18 00:37:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7edx_31075/03_2024/7edx_31075.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7edx_31075/03_2024/7edx_31075.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7edx_31075/03_2024/7edx_31075.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7edx_31075/03_2024/7edx_31075.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7edx_31075/03_2024/7edx_31075.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7edx_31075/03_2024/7edx_31075.pdb" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.033 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 9 6.06 5 P 154 5.49 5 Mg 1 5.21 5 S 455 5.16 5 C 51325 2.51 5 N 14289 2.21 5 O 15557 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 400": "OE1" <-> "OE2" Residue "A GLU 411": "OE1" <-> "OE2" Residue "A GLU 653": "OE1" <-> "OE2" Residue "A GLU 682": "OE1" <-> "OE2" Residue "A ARG 706": "NH1" <-> "NH2" Residue "A GLU 721": "OE1" <-> "OE2" Residue "A GLU 828": "OE1" <-> "OE2" Residue "A GLU 839": "OE1" <-> "OE2" Residue "A GLU 895": "OE1" <-> "OE2" Residue "A ARG 996": "NH1" <-> "NH2" Residue "A ARG 1008": "NH1" <-> "NH2" Residue "A ARG 1030": "NH1" <-> "NH2" Residue "A ARG 1052": "NH1" <-> "NH2" Residue "A GLU 1057": "OE1" <-> "OE2" Residue "A ARG 1181": "NH1" <-> "NH2" Residue "A GLU 1203": "OE1" <-> "OE2" Residue "B GLU 21": "OE1" <-> "OE2" Residue "B ARG 24": "NH1" <-> "NH2" Residue "B PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 76": "NH1" <-> "NH2" Residue "B TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 92": "OE1" <-> "OE2" Residue "B GLU 198": "OE1" <-> "OE2" Residue "B GLU 222": "OE1" <-> "OE2" Residue "B ARG 230": "NH1" <-> "NH2" Residue "B GLU 311": "OE1" <-> "OE2" Residue "B PHE 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 343": "NH1" <-> "NH2" Residue "B GLU 398": "OE1" <-> "OE2" Residue "B ARG 539": "NH1" <-> "NH2" Residue "B ARG 541": "NH1" <-> "NH2" Residue "B GLU 547": "OE1" <-> "OE2" Residue "B GLU 582": "OE1" <-> "OE2" Residue "B GLU 583": "OE1" <-> "OE2" Residue "B ARG 597": "NH1" <-> "NH2" Residue "B ARG 598": "NH1" <-> "NH2" Residue "B GLU 610": "OE1" <-> "OE2" Residue "B ARG 629": "NH1" <-> "NH2" Residue "B PHE 647": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 688": "OE1" <-> "OE2" Residue "B ARG 725": "NH1" <-> "NH2" Residue "B GLU 770": "OE1" <-> "OE2" Residue "B ARG 817": "NH1" <-> "NH2" Residue "B GLU 831": "OE1" <-> "OE2" Residue "B ARG 966": "NH1" <-> "NH2" Residue "B TYR 975": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 881": "NH1" <-> "NH2" Residue "D GLU 884": "OE1" <-> "OE2" Residue "D ARG 909": "NH1" <-> "NH2" Residue "D GLU 960": "OE1" <-> "OE2" Residue "D GLU 962": "OE1" <-> "OE2" Residue "E GLU 226": "OE1" <-> "OE2" Residue "E GLU 235": "OE1" <-> "OE2" Residue "E ARG 347": "NH1" <-> "NH2" Residue "E ARG 450": "NH1" <-> "NH2" Residue "E ARG 452": "NH1" <-> "NH2" Residue "E GLU 563": "OE1" <-> "OE2" Residue "E PHE 600": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 607": "NH1" <-> "NH2" Residue "E GLU 763": "OE1" <-> "OE2" Residue "F GLU 229": "OE1" <-> "OE2" Residue "F ARG 239": "NH1" <-> "NH2" Residue "F GLU 265": "OE1" <-> "OE2" Residue "F ARG 284": "NH1" <-> "NH2" Residue "F ARG 315": "NH1" <-> "NH2" Residue "F ARG 320": "NH1" <-> "NH2" Residue "F ARG 330": "NH1" <-> "NH2" Residue "F ARG 335": "NH1" <-> "NH2" Residue "F ARG 373": "NH1" <-> "NH2" Residue "F ARG 395": "NH1" <-> "NH2" Residue "G GLU 13": "OE1" <-> "OE2" Residue "H ARG 113": "NH1" <-> "NH2" Residue "H ARG 183": "NH1" <-> "NH2" Residue "H ARG 184": "NH1" <-> "NH2" Residue "I TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 119": "NH1" <-> "NH2" Residue "J GLU 124": "OE1" <-> "OE2" Residue "L GLU 121": "OE1" <-> "OE2" Residue "P GLU 191": "OE1" <-> "OE2" Residue "Q GLU 310": "OE1" <-> "OE2" Residue "Q GLU 317": "OE1" <-> "OE2" Residue "R ARG 28": "NH1" <-> "NH2" Residue "R ARG 44": "NH1" <-> "NH2" Residue "R ARG 112": "NH1" <-> "NH2" Residue "R ARG 127": "NH1" <-> "NH2" Residue "R ARG 248": "NH1" <-> "NH2" Residue "R ARG 290": "NH1" <-> "NH2" Residue "d GLU 847": "OE1" <-> "OE2" Residue "d GLU 848": "OE1" <-> "OE2" Residue "d ARG 851": "NH1" <-> "NH2" Residue "d GLU 858": "OE1" <-> "OE2" Residue "d ARG 865": "NH1" <-> "NH2" Residue "d GLU 870": "OE1" <-> "OE2" Residue "d ARG 881": "NH1" <-> "NH2" Residue "d ARG 909": "NH1" <-> "NH2" Residue "d GLU 954": "OE1" <-> "OE2" Residue "d ARG 1057": "NH1" <-> "NH2" Residue "e TYR 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 250": "OE1" <-> "OE2" Residue "e GLU 257": "OE1" <-> "OE2" Residue "e GLU 335": "OE1" <-> "OE2" Residue "e ARG 365": "NH1" <-> "NH2" Residue "e ARG 450": "NH1" <-> "NH2" Residue "e ARG 452": "NH1" <-> "NH2" Residue "e ARG 607": "NH1" <-> "NH2" Residue "e ARG 634": "NH1" <-> "NH2" Residue "e GLU 706": "OE1" <-> "OE2" Residue "f GLU 17": "OE1" <-> "OE2" Residue "f ARG 63": "NH1" <-> "NH2" Residue "f PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 109": "OE1" <-> "OE2" Residue "f GLU 226": "OE1" <-> "OE2" Residue "f GLU 229": "OE1" <-> "OE2" Residue "f ARG 239": "NH1" <-> "NH2" Residue "f ARG 258": "NH1" <-> "NH2" Residue "f ARG 284": "NH1" <-> "NH2" Residue "f ARG 315": "NH1" <-> "NH2" Residue "f ARG 373": "NH1" <-> "NH2" Residue "f ARG 395": "NH1" <-> "NH2" Residue "i ARG 34": "NH1" <-> "NH2" Residue "i GLU 41": "OE1" <-> "OE2" Residue "i ARG 78": "NH1" <-> "NH2" Residue "i ARG 119": "NH1" <-> "NH2" Residue "j GLU 145": "OE1" <-> "OE2" Residue "k ARG 126": "NH1" <-> "NH2" Residue "k GLU 167": "OE1" <-> "OE2" Residue "k GLU 174": "OE1" <-> "OE2" Residue "k ARG 192": "NH1" <-> "NH2" Residue "k ARG 193": "NH1" <-> "NH2" Residue "l GLU 121": "OE1" <-> "OE2" Residue "m ARG 30": "NH1" <-> "NH2" Residue "m ASP 45": "OD1" <-> "OD2" Residue "m ARG 80": "NH1" <-> "NH2" Residue "m GLU 109": "OE1" <-> "OE2" Residue "o GLU 30": "OE1" <-> "OE2" Residue "o GLU 38": "OE1" <-> "OE2" Residue "o GLU 89": "OE1" <-> "OE2" Residue "o GLU 514": "OE1" <-> "OE2" Residue "o GLU 715": "OE1" <-> "OE2" Residue "o ARG 743": "NH1" <-> "NH2" Residue "o ARG 749": "NH1" <-> "NH2" Residue "o GLU 869": "OE1" <-> "OE2" Residue "o GLU 1097": "OE1" <-> "OE2" Residue "o GLU 1349": "OE1" <-> "OE2" Residue "p ARG 101": "NH1" <-> "NH2" Residue "p GLU 266": "OE1" <-> "OE2" Residue "p GLU 346": "OE1" <-> "OE2" Residue "p GLU 381": "OE1" <-> "OE2" Residue "p GLU 551": "OE1" <-> "OE2" Residue "p GLU 609": "OE1" <-> "OE2" Residue "p GLU 647": "OE1" <-> "OE2" Residue "p ARG 770": "NH1" <-> "NH2" Residue "p ARG 841": "NH1" <-> "NH2" Residue "p ARG 1078": "NH1" <-> "NH2" Residue "q ARG 10": "NH1" <-> "NH2" Residue "q PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q GLU 207": "OE1" <-> "OE2" Residue "r GLU 15": "OE1" <-> "OE2" Residue "r GLU 54": "OE1" <-> "OE2" Residue "r GLU 106": "OE1" <-> "OE2" Residue "w GLU 19": "OE1" <-> "OE2" Residue "y GLU 97": "OE1" <-> "OE2" Residue "y GLU 117": "OE1" <-> "OE2" Time to flip residues: 0.18s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 81790 Number of models: 1 Model: "" Number of chains: 46 Chain: "A" Number of atoms: 4927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 602, 4927 Classifications: {'peptide': 602} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 40, 'TRANS': 561} Chain breaks: 8 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 7796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 963, 7796 Classifications: {'peptide': 963} Link IDs: {'PTRANS': 45, 'TRANS': 917} Chain breaks: 1 Chain: "D" Number of atoms: 1377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1377 Classifications: {'peptide': 165} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 161} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "E" Number of atoms: 4364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 546, 4364 Classifications: {'peptide': 546} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 21, 'TRANS': 524} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "F" Number of atoms: 3081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 3081 Classifications: {'peptide': 404} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 24, 'TRANS': 379} Chain breaks: 1 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 161 Unresolved non-hydrogen dihedrals: 105 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 73 Chain: "G" Number of atoms: 1180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1180 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 6, 'TRANS': 138} Chain breaks: 2 Chain: "H" Number of atoms: 1633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1633 Classifications: {'peptide': 209} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 20, 'TRANS': 188} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "I" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 959 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 108} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "J" Number of atoms: 709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 709 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 6, 'TRANS': 82} Chain breaks: 1 Chain: "L" Number of atoms: 622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 622 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 2, 'TRANS': 73} Chain: "O" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 771 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 1, 'TRANS': 95} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "P" Number of atoms: 1412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1412 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 9, 'TRANS': 167} Chain: "Q" Number of atoms: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 996 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 119} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "R" Number of atoms: 1913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1913 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 13, 'TRANS': 234} Chain breaks: 1 Chain: "S" Number of atoms: 1101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1101 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 7, 'TRANS': 126} Chain breaks: 1 Chain: "T" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 876 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 3, 'TRANS': 109} Chain breaks: 1 Chain: "X" Number of atoms: 1582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1582 Classifications: {'DNA': 77} Link IDs: {'rna3p': 76} Chain: "Y" Number of atoms: 1575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1575 Classifications: {'DNA': 77} Link IDs: {'rna3p': 76} Chain: "c" Number of atoms: 1011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1011 Classifications: {'peptide': 127} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 118} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "d" Number of atoms: 1307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1307 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 155} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "e" Number of atoms: 4327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 539, 4327 Classifications: {'peptide': 539} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 516} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "f" Number of atoms: 3081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 3081 Classifications: {'peptide': 403} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 378} Chain breaks: 1 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 109 Unresolved non-hydrogen angles: 138 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 57 Chain: "i" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 967 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 108} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "j" Number of atoms: 759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 759 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 6, 'TRANS': 88} Chain breaks: 1 Chain: "k" Number of atoms: 785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 785 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain: "l" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 876 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 3, 'TRANS': 103} Chain: "m" Number of atoms: 724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 724 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 2, 'TRANS': 84} Chain: "o" Number of atoms: 11308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1427, 11308 Classifications: {'peptide': 1427} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 69, 'TRANS': 1356} Chain breaks: 4 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "p" Number of atoms: 9062 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1134, 9062 Classifications: {'peptide': 1134} Link IDs: {'PTRANS': 53, 'TRANS': 1080} Chain breaks: 2 Chain: "q" Number of atoms: 2059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2059 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 15, 'TRANS': 241} Chain breaks: 1 Chain: "r" Number of atoms: 1005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1005 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 3, 'TRANS': 124} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 36 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 5, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "s" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1720 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 11, 'TRANS': 197} Chain: "t" Number of atoms: 635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 635 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 5, 'TRANS': 73} Chain: "v" Number of atoms: 1186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1186 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 4, 'TRANS': 143} Chain: "w" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 927 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain: "x" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 507 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "y" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 937 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 8, 'TRANS': 108} Chain: "z" Number of atoms: 372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 372 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "u" Number of atoms: 1351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1351 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 10, 'TRANS': 160} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "o" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "p" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "w" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "x" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 29994 SG CYS R 34 74.245 121.636 199.065 1.00 0.00 S ATOM 51175 SG CYS o 71 75.410 117.328 174.393 1.00215.08 S ATOM 51197 SG CYS o 74 75.860 113.206 175.427 1.00208.62 S ATOM 51244 SG CYS o 81 78.526 115.710 175.906 1.00201.81 S ATOM 51479 SG CYS o 111 96.589 103.177 130.921 1.00291.01 S ATOM 51507 SG CYS o 114 92.790 100.859 130.207 1.00287.14 S ATOM 51820 SG CYS o 154 96.288 99.753 129.060 1.00287.91 S ATOM 51853 SG CYS o 184 94.675 102.706 126.283 1.00285.00 S ATOM 70651 SG CYS p1119 78.085 98.354 168.845 1.00179.27 S ATOM 70673 SG CYS p1122 79.818 100.114 166.456 1.00181.25 S ATOM 70788 SG CYS p1137 76.240 101.273 168.064 1.00194.80 S ATOM 70809 SG CYS p1140 77.004 99.788 164.392 1.00200.53 S ATOM 71788 SG CYS q 90 95.431 132.230 237.282 1.00126.45 S ATOM 71823 SG CYS q 94 96.771 134.106 239.767 1.00113.16 S ATOM 71845 SG CYS q 97 99.027 132.123 237.653 1.00107.06 S ATOM 77733 SG CYS w 17 162.224 136.601 129.502 1.00165.50 S ATOM 77757 SG CYS w 20 158.698 137.299 129.420 1.00166.36 S ATOM 77918 SG CYS w 39 158.809 133.633 128.494 1.00170.94 S ATOM 77943 SG CYS w 42 160.678 135.805 126.723 1.00174.09 S ATOM 78295 SG CYS w 86 183.095 130.338 170.366 1.00138.72 S ATOM 78319 SG CYS w 89 184.374 133.535 171.652 1.00141.27 S ATOM 78523 SG CYS w 114 180.655 132.964 172.355 1.00129.58 S ATOM 78558 SG CYS w 119 182.008 133.580 168.943 1.00136.89 S ATOM 78668 SG CYS x 7 129.468 130.219 225.847 1.00 65.12 S ATOM 78692 SG CYS x 10 130.997 127.465 229.452 1.00 73.64 S ATOM 78956 SG CYS x 44 132.440 127.981 226.491 1.00 74.53 S ATOM 78962 SG CYS x 45 132.260 130.831 228.598 1.00 74.88 S ATOM 80099 SG CYS z 19 106.427 161.964 202.754 1.00111.16 S ATOM 80118 SG CYS z 22 106.553 164.764 204.809 1.00114.66 S ATOM 80235 SG CYS z 36 103.734 164.473 202.762 1.00121.32 S Time building chain proxies: 30.94, per 1000 atoms: 0.38 Number of scatterers: 81790 At special positions: 0 Unit cell: (217.3, 240.62, 269.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 9 29.99 S 455 16.00 P 154 15.00 Mg 1 11.99 O 15557 8.00 N 14289 7.00 C 51325 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 945 " - pdb=" SG CYS B 986 " distance=2.07 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 23.71 Conformation dependent library (CDL) restraints added in 10.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN R 401 " pdb="ZN ZN R 401 " - pdb=" SG CYS R 34 " pdb="ZN ZN R 401 " - pdb=" NE2 HIS R 18 " pdb=" ZN o2001 " pdb="ZN ZN o2001 " - pdb=" NE2 HIS o 84 " pdb="ZN ZN o2001 " - pdb=" SG CYS o 74 " pdb="ZN ZN o2001 " - pdb=" SG CYS o 71 " pdb="ZN ZN o2001 " - pdb=" SG CYS o 81 " pdb=" ZN o2002 " pdb="ZN ZN o2002 " - pdb=" SG CYS o 184 " pdb="ZN ZN o2002 " - pdb=" SG CYS o 111 " pdb="ZN ZN o2002 " - pdb=" SG CYS o 114 " pdb="ZN ZN o2002 " - pdb=" SG CYS o 154 " pdb=" ZN p1201 " pdb="ZN ZN p1201 " - pdb=" SG CYS p1122 " pdb="ZN ZN p1201 " - pdb=" SG CYS p1119 " pdb="ZN ZN p1201 " - pdb=" SG CYS p1137 " pdb="ZN ZN p1201 " - pdb=" SG CYS p1140 " pdb=" ZN q 301 " pdb="ZN ZN q 301 " - pdb=" SG CYS q 90 " pdb="ZN ZN q 301 " - pdb=" SG CYS q 94 " pdb="ZN ZN q 301 " - pdb=" SG CYS q 97 " pdb=" ZN w 201 " pdb="ZN ZN w 201 " - pdb=" SG CYS w 39 " pdb="ZN ZN w 201 " - pdb=" SG CYS w 17 " pdb="ZN ZN w 201 " - pdb=" SG CYS w 20 " pdb="ZN ZN w 201 " - pdb=" SG CYS w 42 " pdb=" ZN w 202 " pdb="ZN ZN w 202 " - pdb=" SG CYS w 89 " pdb="ZN ZN w 202 " - pdb=" SG CYS w 119 " pdb="ZN ZN w 202 " - pdb=" SG CYS w 86 " pdb="ZN ZN w 202 " - pdb=" SG CYS w 114 " pdb=" ZN x 101 " pdb="ZN ZN x 101 " - pdb=" SG CYS x 45 " pdb="ZN ZN x 101 " - pdb=" SG CYS x 44 " pdb="ZN ZN x 101 " - pdb=" SG CYS x 7 " pdb="ZN ZN x 101 " - pdb=" SG CYS x 10 " pdb=" ZN z 101 " pdb="ZN ZN z 101 " - pdb=" SG CYS z 22 " pdb="ZN ZN z 101 " - pdb=" SG CYS z 36 " pdb="ZN ZN z 101 " - pdb=" SG CYS z 19 " Number of angles added : 33 19390 Ramachandran restraints generated. 9695 Oldfield, 0 Emsley, 9695 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 18690 Finding SS restraints... Secondary structure from input PDB file: 348 helices and 91 sheets defined 41.1% alpha, 15.0% beta 58 base pairs and 141 stacking pairs defined. Time for finding SS restraints: 19.55 Creating SS restraints... Processing helix chain 'A' and resid 346 through 354 Processing helix chain 'A' and resid 398 through 403 Processing helix chain 'A' and resid 472 through 478 Processing helix chain 'A' and resid 479 through 484 Processing helix chain 'A' and resid 569 through 574 removed outlier: 3.634A pdb=" N TYR A 573 " --> pdb=" O ASN A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 597 Processing helix chain 'A' and resid 608 through 614 Processing helix chain 'A' and resid 640 through 657 Processing helix chain 'A' and resid 667 through 672 removed outlier: 4.036A pdb=" N THR A 672 " --> pdb=" O GLN A 669 " (cutoff:3.500A) Processing helix chain 'A' and resid 796 through 817 Processing helix chain 'A' and resid 826 through 834 removed outlier: 3.977A pdb=" N ILE A 830 " --> pdb=" O ARG A 826 " (cutoff:3.500A) Processing helix chain 'A' and resid 838 through 844 removed outlier: 3.984A pdb=" N ILE A 842 " --> pdb=" O SER A 838 " (cutoff:3.500A) Processing helix chain 'A' and resid 872 through 880 removed outlier: 3.854A pdb=" N VAL A 880 " --> pdb=" O ILE A 876 " (cutoff:3.500A) Processing helix chain 'A' and resid 881 through 901 Processing helix chain 'A' and resid 925 through 929 Processing helix chain 'A' and resid 930 through 944 Processing helix chain 'A' and resid 993 through 998 removed outlier: 3.643A pdb=" N ARG A 997 " --> pdb=" O ALA A 993 " (cutoff:3.500A) Processing helix chain 'A' and resid 1000 through 1011 Processing helix chain 'A' and resid 1013 through 1020 removed outlier: 3.528A pdb=" N ILE A1017 " --> pdb=" O PRO A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1023 through 1035 Processing helix chain 'A' and resid 1056 through 1079 Processing helix chain 'A' and resid 1187 through 1204 removed outlier: 3.601A pdb=" N ILE A1197 " --> pdb=" O ALA A1193 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 117 removed outlier: 3.737A pdb=" N PHE B 106 " --> pdb=" O ASN B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 133 No H-bonds generated for 'chain 'B' and resid 131 through 133' Processing helix chain 'B' and resid 134 through 139 Processing helix chain 'B' and resid 169 through 174 Processing helix chain 'B' and resid 185 through 189 removed outlier: 3.547A pdb=" N PHE B 188 " --> pdb=" O SER B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 247 Processing helix chain 'B' and resid 273 through 281 Processing helix chain 'B' and resid 283 through 295 removed outlier: 3.718A pdb=" N VAL B 287 " --> pdb=" O TYR B 283 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU B 295 " --> pdb=" O TYR B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 330 No H-bonds generated for 'chain 'B' and resid 328 through 330' Processing helix chain 'B' and resid 338 through 356 Processing helix chain 'B' and resid 366 through 409 removed outlier: 4.079A pdb=" N LEU B 370 " --> pdb=" O ASP B 366 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N VAL B 388 " --> pdb=" O LYS B 384 " (cutoff:3.500A) removed outlier: 9.030A pdb=" N ASN B 389 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N GLU B 390 " --> pdb=" O PHE B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 441 removed outlier: 3.558A pdb=" N LEU B 441 " --> pdb=" O PRO B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 464 Processing helix chain 'B' and resid 465 through 484 Processing helix chain 'B' and resid 492 through 495 removed outlier: 3.540A pdb=" N GLN B 495 " --> pdb=" O MET B 492 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 492 through 495' Processing helix chain 'B' and resid 499 through 512 Processing helix chain 'B' and resid 515 through 523 Processing helix chain 'B' and resid 595 through 600 removed outlier: 3.821A pdb=" N ASN B 599 " --> pdb=" O LYS B 595 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS B 600 " --> pdb=" O SER B 596 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 595 through 600' Processing helix chain 'B' and resid 645 through 656 removed outlier: 3.799A pdb=" N GLU B 656 " --> pdb=" O GLN B 652 " (cutoff:3.500A) Processing helix chain 'B' and resid 658 through 669 Processing helix chain 'B' and resid 670 through 672 No H-bonds generated for 'chain 'B' and resid 670 through 672' Processing helix chain 'B' and resid 674 through 686 Processing helix chain 'B' and resid 691 through 709 removed outlier: 3.545A pdb=" N ARG B 695 " --> pdb=" O PHE B 691 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER B 697 " --> pdb=" O ARG B 693 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N PHE B 700 " --> pdb=" O MET B 696 " (cutoff:3.500A) Processing helix chain 'B' and resid 719 through 728 removed outlier: 3.722A pdb=" N CYS B 728 " --> pdb=" O THR B 724 " (cutoff:3.500A) Processing helix chain 'B' and resid 745 through 758 Proline residue: B 754 - end of helix Processing helix chain 'B' and resid 768 through 781 removed outlier: 3.533A pdb=" N THR B 773 " --> pdb=" O LYS B 769 " (cutoff:3.500A) Processing helix chain 'B' and resid 791 through 805 removed outlier: 3.508A pdb=" N SER B 805 " --> pdb=" O ALA B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 823 through 843 removed outlier: 4.202A pdb=" N LEU B 828 " --> pdb=" O PRO B 824 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE B 829 " --> pdb=" O ASP B 825 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU B 842 " --> pdb=" O ASN B 838 " (cutoff:3.500A) Processing helix chain 'B' and resid 848 through 864 Processing helix chain 'B' and resid 871 through 878 Processing helix chain 'B' and resid 883 through 901 Processing helix chain 'B' and resid 903 through 916 removed outlier: 3.522A pdb=" N LEU B 907 " --> pdb=" O SER B 903 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 933 Processing helix chain 'B' and resid 946 through 959 removed outlier: 3.560A pdb=" N VAL B 950 " --> pdb=" O ASN B 946 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 980 Processing helix chain 'D' and resid 874 through 886 removed outlier: 3.681A pdb=" N ARG D 880 " --> pdb=" O ALA D 876 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE D 885 " --> pdb=" O ARG D 881 " (cutoff:3.500A) Processing helix chain 'D' and resid 898 through 922 removed outlier: 3.636A pdb=" N SER D 903 " --> pdb=" O VAL D 899 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASN D 912 " --> pdb=" O GLN D 908 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS D 916 " --> pdb=" O ASN D 912 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N THR D 920 " --> pdb=" O LYS D 916 " (cutoff:3.500A) Processing helix chain 'D' and resid 939 through 969 removed outlier: 4.467A pdb=" N GLN D 943 " --> pdb=" O ASP D 939 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU D 944 " --> pdb=" O VAL D 940 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LYS D 945 " --> pdb=" O ARG D 941 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N PHE D 946 " --> pdb=" O ALA D 942 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU D 960 " --> pdb=" O GLN D 956 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLN D 961 " --> pdb=" O ARG D 957 " (cutoff:3.500A) Processing helix chain 'D' and resid 980 through 1010 removed outlier: 3.503A pdb=" N GLN D 998 " --> pdb=" O GLN D 994 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N ASP D1003 " --> pdb=" O MET D 999 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ALA D1004 " --> pdb=" O ARG D1000 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ALA D1010 " --> pdb=" O LEU D1006 " (cutoff:3.500A) Processing helix chain 'D' and resid 1059 through 1066 removed outlier: 3.621A pdb=" N LEU D1063 " --> pdb=" O ASN D1059 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N CYS D1066 " --> pdb=" O ASP D1062 " (cutoff:3.500A) Processing helix chain 'D' and resid 1076 through 1083 Processing helix chain 'E' and resid 210 through 212 No H-bonds generated for 'chain 'E' and resid 210 through 212' Processing helix chain 'E' and resid 213 through 227 removed outlier: 3.838A pdb=" N SER E 219 " --> pdb=" O GLU E 215 " (cutoff:3.500A) Processing helix chain 'E' and resid 229 through 237 removed outlier: 3.812A pdb=" N ALA E 234 " --> pdb=" O ASP E 230 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N GLU E 235 " --> pdb=" O CYS E 231 " (cutoff:3.500A) Processing helix chain 'E' and resid 239 through 254 removed outlier: 3.695A pdb=" N LEU E 243 " --> pdb=" O LEU E 239 " (cutoff:3.500A) Processing helix chain 'E' and resid 257 through 268 removed outlier: 3.750A pdb=" N SER E 262 " --> pdb=" O ASN E 258 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N PHE E 263 " --> pdb=" O GLU E 259 " (cutoff:3.500A) Processing helix chain 'E' and resid 272 through 274 No H-bonds generated for 'chain 'E' and resid 272 through 274' Processing helix chain 'E' and resid 275 through 285 removed outlier: 3.654A pdb=" N ARG E 280 " --> pdb=" O GLN E 276 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N VAL E 281 " --> pdb=" O ASP E 277 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU E 282 " --> pdb=" O ASP E 278 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER E 284 " --> pdb=" O ARG E 280 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 292 removed outlier: 3.800A pdb=" N MET E 291 " --> pdb=" O LYS E 287 " (cutoff:3.500A) Processing helix chain 'E' and resid 296 through 303 removed outlier: 3.711A pdb=" N THR E 302 " --> pdb=" O LEU E 298 " (cutoff:3.500A) Processing helix chain 'E' and resid 311 through 319 removed outlier: 4.311A pdb=" N LEU E 316 " --> pdb=" O ASP E 312 " (cutoff:3.500A) Processing helix chain 'E' and resid 328 through 337 Processing helix chain 'E' and resid 348 through 353 Processing helix chain 'E' and resid 433 through 449 removed outlier: 3.535A pdb=" N LYS E 440 " --> pdb=" O ASP E 436 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE E 441 " --> pdb=" O LYS E 437 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N MET E 442 " --> pdb=" O LEU E 438 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS E 445 " --> pdb=" O ILE E 441 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU E 446 " --> pdb=" O MET E 442 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LYS E 449 " --> pdb=" O LYS E 445 " (cutoff:3.500A) Processing helix chain 'E' and resid 509 through 516 removed outlier: 3.698A pdb=" N LEU E 515 " --> pdb=" O SER E 511 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE E 516 " --> pdb=" O ASP E 512 " (cutoff:3.500A) Processing helix chain 'E' and resid 522 through 527 removed outlier: 3.821A pdb=" N ILE E 527 " --> pdb=" O VAL E 523 " (cutoff:3.500A) Processing helix chain 'E' and resid 764 through 768 Processing helix chain 'F' and resid 15 through 25 removed outlier: 3.749A pdb=" N MET F 19 " --> pdb=" O PRO F 15 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N VAL F 21 " --> pdb=" O GLU F 17 " (cutoff:3.500A) Processing helix chain 'F' and resid 32 through 61 removed outlier: 3.554A pdb=" N LEU F 39 " --> pdb=" O THR F 35 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR F 40 " --> pdb=" O CYS F 36 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLU F 42 " --> pdb=" O LEU F 38 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N SER F 44 " --> pdb=" O THR F 40 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LYS F 56 " --> pdb=" O GLN F 52 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N PHE F 57 " --> pdb=" O ASP F 53 " (cutoff:3.500A) Processing helix chain 'F' and resid 67 through 78 removed outlier: 4.196A pdb=" N ILE F 71 " --> pdb=" O THR F 67 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ASP F 72 " --> pdb=" O THR F 68 " (cutoff:3.500A) Processing helix chain 'F' and resid 115 through 120 removed outlier: 3.532A pdb=" N THR F 120 " --> pdb=" O ASP F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 217 through 231 Processing helix chain 'F' and resid 235 through 249 Processing helix chain 'F' and resid 250 through 253 removed outlier: 4.354A pdb=" N TYR F 253 " --> pdb=" O PRO F 250 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 250 through 253' Processing helix chain 'F' and resid 255 through 270 Processing helix chain 'F' and resid 275 through 291 Processing helix chain 'F' and resid 300 through 314 removed outlier: 3.865A pdb=" N LEU F 304 " --> pdb=" O TYR F 300 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ILE F 305 " --> pdb=" O VAL F 301 " (cutoff:3.500A) Proline residue: F 306 - end of helix removed outlier: 3.814A pdb=" N CYS F 311 " --> pdb=" O ALA F 307 " (cutoff:3.500A) Processing helix chain 'F' and resid 323 through 344 Processing helix chain 'F' and resid 351 through 364 Processing helix chain 'F' and resid 369 through 382 Processing helix chain 'F' and resid 384 through 396 removed outlier: 4.169A pdb=" N ILE F 388 " --> pdb=" O GLY F 384 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LYS F 389 " --> pdb=" O HIS F 385 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N THR F 390 " --> pdb=" O ASP F 386 " (cutoff:3.500A) Proline residue: F 394 - end of helix Processing helix chain 'F' and resid 397 through 409 Processing helix chain 'F' and resid 415 through 438 Proline residue: F 433 - end of helix Processing helix chain 'F' and resid 446 through 452 removed outlier: 3.595A pdb=" N PHE F 452 " --> pdb=" O ARG F 449 " (cutoff:3.500A) Processing helix chain 'F' and resid 455 through 473 Processing helix chain 'G' and resid 21 through 35 Processing helix chain 'G' and resid 37 through 42 removed outlier: 3.682A pdb=" N ASP G 41 " --> pdb=" O VAL G 37 " (cutoff:3.500A) Processing helix chain 'G' and resid 162 through 174 Processing helix chain 'H' and resid 27 through 45 removed outlier: 4.759A pdb=" N ARG H 33 " --> pdb=" O TYR H 29 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N THR H 36 " --> pdb=" O ALA H 32 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL H 39 " --> pdb=" O ARG H 35 " (cutoff:3.500A) Processing helix chain 'H' and resid 54 through 83 removed outlier: 3.516A pdb=" N LYS H 77 " --> pdb=" O GLY H 73 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR H 83 " --> pdb=" O TYR H 79 " (cutoff:3.500A) Processing helix chain 'H' and resid 97 through 101 Processing helix chain 'H' and resid 103 through 105 No H-bonds generated for 'chain 'H' and resid 103 through 105' Processing helix chain 'H' and resid 106 through 112 removed outlier: 3.872A pdb=" N LYS H 112 " --> pdb=" O PRO H 108 " (cutoff:3.500A) Processing helix chain 'H' and resid 155 through 160 removed outlier: 4.364A pdb=" N TYR H 159 " --> pdb=" O ASP H 155 " (cutoff:3.500A) Processing helix chain 'H' and resid 171 through 197 Processing helix chain 'H' and resid 221 through 228 removed outlier: 4.263A pdb=" N THR H 225 " --> pdb=" O ILE H 221 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU H 228 " --> pdb=" O LEU H 224 " (cutoff:3.500A) Processing helix chain 'I' and resid 14 through 26 removed outlier: 3.575A pdb=" N MET I 18 " --> pdb=" O LYS I 14 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA I 20 " --> pdb=" O ALA I 16 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLN I 21 " --> pdb=" O GLN I 17 " (cutoff:3.500A) Processing helix chain 'I' and resid 32 through 62 removed outlier: 4.413A pdb=" N ILE I 36 " --> pdb=" O GLU I 32 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ASN I 37 " --> pdb=" O PRO I 33 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN I 38 " --> pdb=" O ARG I 34 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ASP I 52 " --> pdb=" O THR I 48 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASP I 53 " --> pdb=" O THR I 49 " (cutoff:3.500A) Processing helix chain 'I' and resid 67 through 77 removed outlier: 3.551A pdb=" N VAL I 71 " --> pdb=" O ASP I 67 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN I 76 " --> pdb=" O ARG I 72 " (cutoff:3.500A) Processing helix chain 'I' and resid 88 through 100 removed outlier: 3.674A pdb=" N ASP I 94 " --> pdb=" O ASP I 90 " (cutoff:3.500A) Processing helix chain 'J' and resid 115 through 121 Processing helix chain 'J' and resid 131 through 141 removed outlier: 3.689A pdb=" N TYR J 137 " --> pdb=" O ALA J 133 " (cutoff:3.500A) Processing helix chain 'J' and resid 148 through 170 removed outlier: 3.624A pdb=" N ILE J 152 " --> pdb=" O ASP J 148 " (cutoff:3.500A) Processing helix chain 'J' and resid 171 through 176 removed outlier: 3.727A pdb=" N MET J 176 " --> pdb=" O GLN J 172 " (cutoff:3.500A) Processing helix chain 'J' and resid 196 through 204 Proline residue: J 202 - end of helix Processing helix chain 'L' and resid 61 through 71 removed outlier: 3.951A pdb=" N VAL L 70 " --> pdb=" O LEU L 66 " (cutoff:3.500A) Processing helix chain 'L' and resid 77 through 106 removed outlier: 3.672A pdb=" N MET L 83 " --> pdb=" O ASP L 79 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ALA L 98 " --> pdb=" O SER L 94 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLN L 101 " --> pdb=" O THR L 97 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU L 102 " --> pdb=" O ALA L 98 " (cutoff:3.500A) Processing helix chain 'L' and resid 112 through 123 removed outlier: 3.950A pdb=" N VAL L 116 " --> pdb=" O GLU L 112 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N HIS L 119 " --> pdb=" O ASP L 115 " (cutoff:3.500A) Processing helix chain 'O' and resid 3 through 8 removed outlier: 4.242A pdb=" N TYR O 6 " --> pdb=" O TYR O 3 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ARG O 7 " --> pdb=" O GLN O 4 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ASN O 8 " --> pdb=" O LEU O 5 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 3 through 8' Processing helix chain 'O' and resid 9 through 25 Processing helix chain 'O' and resid 31 through 50 Processing helix chain 'P' and resid 179 through 187 removed outlier: 3.518A pdb=" N ILE P 183 " --> pdb=" O ASP P 179 " (cutoff:3.500A) Processing helix chain 'P' and resid 226 through 245 removed outlier: 3.819A pdb=" N LEU P 244 " --> pdb=" O VAL P 240 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLY P 245 " --> pdb=" O VAL P 241 " (cutoff:3.500A) Processing helix chain 'P' and resid 269 through 277 removed outlier: 3.576A pdb=" N LEU P 273 " --> pdb=" O ARG P 269 " (cutoff:3.500A) Processing helix chain 'P' and resid 317 through 335 removed outlier: 4.035A pdb=" N ILE P 321 " --> pdb=" O VAL P 317 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N TYR P 322 " --> pdb=" O ARG P 318 " (cutoff:3.500A) Proline residue: P 330 - end of helix Processing helix chain 'Q' and resid 10 through 33 removed outlier: 4.803A pdb=" N ASP Q 27 " --> pdb=" O ASN Q 23 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N ILE Q 28 " --> pdb=" O ASP Q 24 " (cutoff:3.500A) Processing helix chain 'Q' and resid 35 through 54 removed outlier: 3.732A pdb=" N LEU Q 39 " --> pdb=" O ASP Q 35 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU Q 50 " --> pdb=" O TRP Q 46 " (cutoff:3.500A) Processing helix chain 'Q' and resid 58 through 63 Processing helix chain 'Q' and resid 323 through 328 Processing helix chain 'R' and resid 111 through 126 Processing helix chain 'R' and resid 131 through 149 Processing helix chain 'R' and resid 155 through 171 Processing helix chain 'R' and resid 176 through 183 removed outlier: 3.513A pdb=" N VAL R 183 " --> pdb=" O GLU R 179 " (cutoff:3.500A) Processing helix chain 'R' and resid 187 through 203 Processing helix chain 'R' and resid 211 through 222 removed outlier: 3.848A pdb=" N SER R 216 " --> pdb=" O GLY R 212 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N ARG R 217 " --> pdb=" O ASP R 213 " (cutoff:3.500A) Processing helix chain 'R' and resid 225 through 242 Processing helix chain 'R' and resid 249 through 264 Processing helix chain 'R' and resid 270 through 279 Processing helix chain 'R' and resid 281 through 293 Processing helix chain 'R' and resid 295 through 300 removed outlier: 3.885A pdb=" N PHE R 300 " --> pdb=" O ALA R 296 " (cutoff:3.500A) Processing helix chain 'R' and resid 309 through 313 Processing helix chain 'S' and resid 6 through 10 Processing helix chain 'S' and resid 34 through 36 No H-bonds generated for 'chain 'S' and resid 34 through 36' Processing helix chain 'S' and resid 38 through 42 Processing helix chain 'S' and resid 156 through 173 Processing helix chain 'T' and resid 9 through 14 Processing helix chain 'T' and resid 25 through 32 Processing helix chain 'T' and resid 121 through 123 No H-bonds generated for 'chain 'T' and resid 121 through 123' Processing helix chain 'T' and resid 124 through 129 Processing helix chain 'c' and resid 2 through 16 Processing helix chain 'c' and resid 16 through 21 removed outlier: 3.553A pdb=" N ALA c 20 " --> pdb=" O GLN c 16 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU c 21 " --> pdb=" O ILE c 17 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 16 through 21' Processing helix chain 'c' and resid 28 through 56 removed outlier: 3.561A pdb=" N HIS c 32 " --> pdb=" O LEU c 28 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LEU c 33 " --> pdb=" O SER c 29 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU c 34 " --> pdb=" O ALA c 30 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASP c 36 " --> pdb=" O HIS c 32 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLN c 43 " --> pdb=" O GLN c 39 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N SER c 53 " --> pdb=" O CYS c 49 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N TYR c 56 " --> pdb=" O TYR c 52 " (cutoff:3.500A) Processing helix chain 'c' and resid 62 through 74 removed outlier: 3.935A pdb=" N GLN c 71 " --> pdb=" O GLY c 67 " (cutoff:3.500A) Processing helix chain 'c' and resid 76 through 87 removed outlier: 3.606A pdb=" N GLU c 81 " --> pdb=" O LEU c 77 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASP c 82 " --> pdb=" O HIS c 78 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASN c 86 " --> pdb=" O ASP c 82 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE c 87 " --> pdb=" O TYR c 83 " (cutoff:3.500A) Processing helix chain 'd' and resid 844 through 849 removed outlier: 3.526A pdb=" N GLU d 848 " --> pdb=" O ASN d 844 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER d 849 " --> pdb=" O LEU d 845 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 844 through 849' Processing helix chain 'd' and resid 849 through 855 removed outlier: 4.154A pdb=" N LEU d 853 " --> pdb=" O SER d 849 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N THR d 855 " --> pdb=" O ARG d 851 " (cutoff:3.500A) Processing helix chain 'd' and resid 856 through 858 No H-bonds generated for 'chain 'd' and resid 856 through 858' Processing helix chain 'd' and resid 874 through 885 removed outlier: 3.676A pdb=" N ARG d 880 " --> pdb=" O ALA d 876 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU d 883 " --> pdb=" O GLN d 879 " (cutoff:3.500A) Processing helix chain 'd' and resid 898 through 922 removed outlier: 3.548A pdb=" N HIS d 904 " --> pdb=" O SER d 900 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLN d 907 " --> pdb=" O SER d 903 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU d 913 " --> pdb=" O ARG d 909 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU d 919 " --> pdb=" O GLU d 915 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THR d 920 " --> pdb=" O LYS d 916 " (cutoff:3.500A) Processing helix chain 'd' and resid 923 through 926 Processing helix chain 'd' and resid 945 through 954 Processing helix chain 'd' and resid 954 through 966 removed outlier: 3.502A pdb=" N LYS d 958 " --> pdb=" O GLU d 954 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU d 962 " --> pdb=" O LYS d 958 " (cutoff:3.500A) Processing helix chain 'd' and resid 1059 through 1069 removed outlier: 3.755A pdb=" N LEU d1063 " --> pdb=" O ASN d1059 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N CYS d1066 " --> pdb=" O ASP d1062 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASN d1069 " --> pdb=" O PHE d1065 " (cutoff:3.500A) Processing helix chain 'd' and resid 1076 through 1083 removed outlier: 3.688A pdb=" N TYR d1080 " --> pdb=" O SER d1076 " (cutoff:3.500A) Processing helix chain 'e' and resid 210 through 212 No H-bonds generated for 'chain 'e' and resid 210 through 212' Processing helix chain 'e' and resid 213 through 218 removed outlier: 3.641A pdb=" N TYR e 217 " --> pdb=" O MET e 213 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N TYR e 218 " --> pdb=" O TYR e 214 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 213 through 218' Processing helix chain 'e' and resid 220 through 227 Processing helix chain 'e' and resid 236 through 240 removed outlier: 3.712A pdb=" N LEU e 239 " --> pdb=" O LEU e 236 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE e 240 " --> pdb=" O SER e 237 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 236 through 240' Processing helix chain 'e' and resid 243 through 248 Processing helix chain 'e' and resid 257 through 268 removed outlier: 4.228A pdb=" N SER e 262 " --> pdb=" O ASN e 258 " (cutoff:3.500A) Processing helix chain 'e' and resid 281 through 285 Processing helix chain 'e' and resid 287 through 292 removed outlier: 3.905A pdb=" N MET e 291 " --> pdb=" O LYS e 287 " (cutoff:3.500A) Processing helix chain 'e' and resid 310 through 322 removed outlier: 3.604A pdb=" N GLN e 315 " --> pdb=" O ARG e 311 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N LEU e 316 " --> pdb=" O ASP e 312 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU e 317 " --> pdb=" O SER e 313 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLN e 322 " --> pdb=" O LYS e 318 " (cutoff:3.500A) Processing helix chain 'e' and resid 329 through 334 removed outlier: 3.925A pdb=" N VAL e 333 " --> pdb=" O ILE e 329 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLN e 334 " --> pdb=" O TRP e 330 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 329 through 334' Processing helix chain 'e' and resid 433 through 438 Processing helix chain 'e' and resid 438 through 446 removed outlier: 3.505A pdb=" N GLU e 446 " --> pdb=" O MET e 442 " (cutoff:3.500A) Processing helix chain 'e' and resid 511 through 515 Processing helix chain 'e' and resid 522 through 527 removed outlier: 3.504A pdb=" N ARG e 526 " --> pdb=" O ASP e 522 " (cutoff:3.500A) Processing helix chain 'f' and resid 16 through 27 removed outlier: 3.720A pdb=" N LYS f 20 " --> pdb=" O SER f 16 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL f 21 " --> pdb=" O GLU f 17 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL f 22 " --> pdb=" O SER f 18 " (cutoff:3.500A) Processing helix chain 'f' and resid 32 through 61 removed outlier: 3.536A pdb=" N ASP f 41 " --> pdb=" O GLN f 37 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N GLU f 42 " --> pdb=" O LEU f 38 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N TYR f 45 " --> pdb=" O ASP f 41 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LYS f 48 " --> pdb=" O SER f 44 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASP f 53 " --> pdb=" O GLU f 49 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LYS f 56 " --> pdb=" O GLN f 52 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N PHE f 57 " --> pdb=" O ASP f 53 " (cutoff:3.500A) Processing helix chain 'f' and resid 67 through 76 removed outlier: 4.017A pdb=" N ILE f 71 " --> pdb=" O THR f 67 " (cutoff:3.500A) Processing helix chain 'f' and resid 114 through 119 Processing helix chain 'f' and resid 217 through 231 removed outlier: 3.540A pdb=" N CYS f 231 " --> pdb=" O ILE f 227 " (cutoff:3.500A) Processing helix chain 'f' and resid 235 through 248 removed outlier: 3.626A pdb=" N ARG f 239 " --> pdb=" O CYS f 235 " (cutoff:3.500A) Processing helix chain 'f' and resid 255 through 269 Processing helix chain 'f' and resid 275 through 291 removed outlier: 3.526A pdb=" N LEU f 279 " --> pdb=" O ASN f 275 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASP f 291 " --> pdb=" O LYS f 287 " (cutoff:3.500A) Processing helix chain 'f' and resid 300 through 314 removed outlier: 3.631A pdb=" N LEU f 304 " --> pdb=" O TYR f 300 " (cutoff:3.500A) Proline residue: f 306 - end of helix Processing helix chain 'f' and resid 325 through 341 removed outlier: 4.121A pdb=" N LEU f 329 " --> pdb=" O ASN f 325 " (cutoff:3.500A) Processing helix chain 'f' and resid 350 through 364 Processing helix chain 'f' and resid 369 through 384 removed outlier: 4.057A pdb=" N GLY f 384 " --> pdb=" O LEU f 380 " (cutoff:3.500A) Processing helix chain 'f' and resid 384 through 391 removed outlier: 3.546A pdb=" N ILE f 388 " --> pdb=" O GLY f 384 " (cutoff:3.500A) Processing helix chain 'f' and resid 392 through 396 removed outlier: 3.690A pdb=" N LEU f 396 " --> pdb=" O LEU f 393 " (cutoff:3.500A) Processing helix chain 'f' and resid 397 through 404 removed outlier: 3.693A pdb=" N GLU f 401 " --> pdb=" O GLN f 397 " (cutoff:3.500A) Processing helix chain 'f' and resid 417 through 438 Proline residue: f 433 - end of helix Processing helix chain 'f' and resid 445 through 450 Processing helix chain 'f' and resid 454 through 473 Processing helix chain 'i' and resid 18 through 26 Processing helix chain 'i' and resid 33 through 61 removed outlier: 4.305A pdb=" N ASN i 37 " --> pdb=" O PRO i 33 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU i 41 " --> pdb=" O ASN i 37 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA i 43 " --> pdb=" O MET i 39 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL i 47 " --> pdb=" O ALA i 43 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ASP i 52 " --> pdb=" O THR i 48 " (cutoff:3.500A) Processing helix chain 'i' and resid 67 through 77 removed outlier: 3.511A pdb=" N VAL i 71 " --> pdb=" O ASP i 67 " (cutoff:3.500A) Processing helix chain 'i' and resid 88 through 100 removed outlier: 3.966A pdb=" N ASP i 94 " --> pdb=" O ASP i 90 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLN i 98 " --> pdb=" O ASP i 94 " (cutoff:3.500A) Processing helix chain 'j' and resid 115 through 121 removed outlier: 3.722A pdb=" N LEU j 120 " --> pdb=" O LEU j 116 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N MET j 121 " --> pdb=" O VAL j 117 " (cutoff:3.500A) Processing helix chain 'j' and resid 131 through 139 Processing helix chain 'j' and resid 151 through 175 removed outlier: 3.761A pdb=" N LEU j 157 " --> pdb=" O ARG j 153 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE j 162 " --> pdb=" O ALA j 158 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE j 163 " --> pdb=" O ALA j 159 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ASN j 168 " --> pdb=" O SER j 164 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU j 171 " --> pdb=" O ALA j 167 " (cutoff:3.500A) Processing helix chain 'j' and resid 196 through 205 Proline residue: j 202 - end of helix removed outlier: 3.573A pdb=" N SER j 205 " --> pdb=" O THR j 201 " (cutoff:3.500A) Processing helix chain 'k' and resid 116 through 127 removed outlier: 3.502A pdb=" N ARG k 125 " --> pdb=" O TYR k 121 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER k 127 " --> pdb=" O MET k 123 " (cutoff:3.500A) Processing helix chain 'k' and resid 130 through 143 removed outlier: 4.103A pdb=" N ARG k 136 " --> pdb=" O ALA k 132 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE k 141 " --> pdb=" O LEU k 137 " (cutoff:3.500A) Processing helix chain 'k' and resid 147 through 176 removed outlier: 3.607A pdb=" N ALA k 153 " --> pdb=" O ASN k 149 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER k 158 " --> pdb=" O MET k 154 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LYS k 159 " --> pdb=" O SER k 155 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLU k 167 " --> pdb=" O GLY k 163 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU k 168 " --> pdb=" O GLU k 164 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ASP k 171 " --> pdb=" O GLU k 167 " (cutoff:3.500A) Processing helix chain 'k' and resid 184 through 197 removed outlier: 3.607A pdb=" N LYS k 197 " --> pdb=" O ARG k 193 " (cutoff:3.500A) Processing helix chain 'l' and resid 61 through 69 Processing helix chain 'l' and resid 77 through 106 removed outlier: 3.598A pdb=" N MET l 83 " --> pdb=" O ASP l 79 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLN l 86 " --> pdb=" O GLU l 82 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA l 88 " --> pdb=" O LEU l 84 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASP l 89 " --> pdb=" O LEU l 85 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU l 93 " --> pdb=" O ASP l 89 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA l 98 " --> pdb=" O SER l 94 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N GLN l 101 " --> pdb=" O THR l 97 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N LEU l 102 " --> pdb=" O ALA l 98 " (cutoff:3.500A) Processing helix chain 'l' and resid 113 through 123 removed outlier: 3.894A pdb=" N LEU l 118 " --> pdb=" O LYS l 114 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N HIS l 119 " --> pdb=" O ASP l 115 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU l 120 " --> pdb=" O VAL l 116 " (cutoff:3.500A) Processing helix chain 'l' and resid 145 through 161 removed outlier: 3.793A pdb=" N ALA l 153 " --> pdb=" O LYS l 149 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU l 154 " --> pdb=" O GLN l 150 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE l 155 " --> pdb=" O ARG l 151 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ARG l 156 " --> pdb=" O MET l 152 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N LYS l 157 " --> pdb=" O ALA l 153 " (cutoff:3.500A) Processing helix chain 'm' and resid 34 through 43 removed outlier: 3.733A pdb=" N CYS m 38 " --> pdb=" O LYS m 34 " (cutoff:3.500A) Processing helix chain 'm' and resid 50 through 67 removed outlier: 3.602A pdb=" N ILE m 56 " --> pdb=" O GLU m 52 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASP m 59 " --> pdb=" O ASP m 55 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE m 62 " --> pdb=" O GLU m 58 " (cutoff:3.500A) Processing helix chain 'm' and resid 93 through 99 removed outlier: 3.878A pdb=" N PHE m 97 " --> pdb=" O ASP m 93 " (cutoff:3.500A) Processing helix chain 'm' and resid 100 through 106 Processing helix chain 'o' and resid 27 through 35 Processing helix chain 'o' and resid 99 through 110 Processing helix chain 'o' and resid 123 through 132 removed outlier: 3.746A pdb=" N LYS o 127 " --> pdb=" O ASN o 123 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS o 132 " --> pdb=" O ASP o 128 " (cutoff:3.500A) Processing helix chain 'o' and resid 136 through 145 Processing helix chain 'o' and resid 217 through 226 Processing helix chain 'o' and resid 231 through 236 Processing helix chain 'o' and resid 244 through 249 Processing helix chain 'o' and resid 276 through 294 removed outlier: 3.573A pdb=" N ARG o 292 " --> pdb=" O ASN o 288 " (cutoff:3.500A) Processing helix chain 'o' and resid 301 through 319 removed outlier: 3.863A pdb=" N GLU o 305 " --> pdb=" O HIS o 301 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU o 309 " --> pdb=" O GLU o 305 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N VAL o 318 " --> pdb=" O VAL o 314 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ASP o 319 " --> pdb=" O ALA o 315 " (cutoff:3.500A) Processing helix chain 'o' and resid 338 through 343 removed outlier: 3.638A pdb=" N LEU o 343 " --> pdb=" O LEU o 339 " (cutoff:3.500A) Processing helix chain 'o' and resid 381 through 386 Processing helix chain 'o' and resid 398 through 408 removed outlier: 3.743A pdb=" N ARG o 408 " --> pdb=" O GLU o 404 " (cutoff:3.500A) Processing helix chain 'o' and resid 434 through 438 removed outlier: 3.728A pdb=" N ASP o 437 " --> pdb=" O LYS o 434 " (cutoff:3.500A) Processing helix chain 'o' and resid 488 through 493 removed outlier: 3.696A pdb=" N TYR o 492 " --> pdb=" O VAL o 488 " (cutoff:3.500A) Processing helix chain 'o' and resid 509 through 519 Processing helix chain 'o' and resid 520 through 524 Processing helix chain 'o' and resid 538 through 549 removed outlier: 4.051A pdb=" N THR o 543 " --> pdb=" O GLN o 539 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA o 544 " --> pdb=" O ASP o 540 " (cutoff:3.500A) Processing helix chain 'o' and resid 556 through 565 removed outlier: 3.528A pdb=" N VAL o 560 " --> pdb=" O GLU o 556 " (cutoff:3.500A) Processing helix chain 'o' and resid 588 through 593 Processing helix chain 'o' and resid 641 through 646 Processing helix chain 'o' and resid 651 through 660 Processing helix chain 'o' and resid 664 through 684 removed outlier: 4.535A pdb=" N ILE o 682 " --> pdb=" O ASN o 678 " (cutoff:3.500A) Processing helix chain 'o' and resid 695 through 722 Processing helix chain 'o' and resid 732 through 759 removed outlier: 3.505A pdb=" N SER o 759 " --> pdb=" O SER o 755 " (cutoff:3.500A) Processing helix chain 'o' and resid 764 through 772 removed outlier: 3.509A pdb=" N SER o 768 " --> pdb=" O ASN o 764 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N MET o 769 " --> pdb=" O ASN o 765 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N SER o 772 " --> pdb=" O SER o 768 " (cutoff:3.500A) Processing helix chain 'o' and resid 777 through 786 removed outlier: 3.906A pdb=" N ILE o 781 " --> pdb=" O SER o 777 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N SER o 782 " --> pdb=" O LYS o 778 " (cutoff:3.500A) Processing helix chain 'o' and resid 832 through 868 removed outlier: 4.223A pdb=" N THR o 850 " --> pdb=" O GLY o 846 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA o 851 " --> pdb=" O LEU o 847 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N THR o 854 " --> pdb=" O THR o 850 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N ALA o 855 " --> pdb=" O ALA o 851 " (cutoff:3.500A) Processing helix chain 'o' and resid 890 through 894 Processing helix chain 'o' and resid 912 through 920 removed outlier: 3.758A pdb=" N GLU o 917 " --> pdb=" O ASN o 913 " (cutoff:3.500A) Processing helix chain 'o' and resid 928 through 934 Processing helix chain 'o' and resid 935 through 943 removed outlier: 3.679A pdb=" N LYS o 940 " --> pdb=" O GLU o 936 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ASP o 941 " --> pdb=" O ASP o 937 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU o 943 " --> pdb=" O VAL o 939 " (cutoff:3.500A) Processing helix chain 'o' and resid 945 through 970 removed outlier: 3.753A pdb=" N GLU o 955 " --> pdb=" O GLU o 951 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N PHE o 956 " --> pdb=" O LEU o 952 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLU o 957 " --> pdb=" O GLU o 953 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASP o 962 " --> pdb=" O ARG o 958 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N VAL o 968 " --> pdb=" O GLU o 964 " (cutoff:3.500A) Processing helix chain 'o' and resid 983 through 994 removed outlier: 3.635A pdb=" N LYS o 992 " --> pdb=" O TRP o 988 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N PHE o 994 " --> pdb=" O ALA o 990 " (cutoff:3.500A) Processing helix chain 'o' and resid 1005 through 1019 removed outlier: 3.514A pdb=" N LYS o1019 " --> pdb=" O GLU o1015 " (cutoff:3.500A) Processing helix chain 'o' and resid 1032 through 1038 Processing helix chain 'o' and resid 1039 through 1049 Processing helix chain 'o' and resid 1052 through 1057 Processing helix chain 'o' and resid 1062 through 1077 removed outlier: 3.772A pdb=" N ASP o1066 " --> pdb=" O GLY o1062 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N TRP o1067 " --> pdb=" O GLU o1063 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU o1068 " --> pdb=" O ALA o1064 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU o1073 " --> pdb=" O LEU o1069 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER o1074 " --> pdb=" O GLY o1070 " (cutoff:3.500A) Processing helix chain 'o' and resid 1086 through 1097 removed outlier: 3.512A pdb=" N SER o1094 " --> pdb=" O LEU o1090 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LEU o1095 " --> pdb=" O ALA o1091 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY o1096 " --> pdb=" O ALA o1092 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU o1097 " --> pdb=" O GLN o1093 " (cutoff:3.500A) Processing helix chain 'o' and resid 1098 through 1100 No H-bonds generated for 'chain 'o' and resid 1098 through 1100' Processing helix chain 'o' and resid 1120 through 1129 Processing helix chain 'o' and resid 1145 through 1149 Processing helix chain 'o' and resid 1150 through 1162 Processing helix chain 'o' and resid 1165 through 1168 removed outlier: 3.659A pdb=" N LYS o1168 " --> pdb=" O THR o1165 " (cutoff:3.500A) No H-bonds generated for 'chain 'o' and resid 1165 through 1168' Processing helix chain 'o' and resid 1189 through 1198 Processing helix chain 'o' and resid 1217 through 1223 Processing helix chain 'o' and resid 1227 through 1237 removed outlier: 3.943A pdb=" N ILE o1231 " --> pdb=" O THR o1227 " (cutoff:3.500A) Processing helix chain 'o' and resid 1263 through 1266 Processing helix chain 'o' and resid 1280 through 1293 removed outlier: 3.727A pdb=" N LEU o1293 " --> pdb=" O GLU o1289 " (cutoff:3.500A) Processing helix chain 'o' and resid 1342 through 1347 removed outlier: 3.565A pdb=" N VAL o1346 " --> pdb=" O SER o1342 " (cutoff:3.500A) Processing helix chain 'o' and resid 1361 through 1369 removed outlier: 3.644A pdb=" N ILE o1365 " --> pdb=" O ASP o1361 " (cutoff:3.500A) Processing helix chain 'o' and resid 1371 through 1387 Processing helix chain 'o' and resid 1388 through 1390 No H-bonds generated for 'chain 'o' and resid 1388 through 1390' Processing helix chain 'o' and resid 1394 through 1405 removed outlier: 4.194A pdb=" N LEU o1398 " --> pdb=" O ASN o1394 " (cutoff:3.500A) Processing helix chain 'o' and resid 1415 through 1420 Processing helix chain 'o' and resid 1425 through 1430 removed outlier: 3.960A pdb=" N LYS o1429 " --> pdb=" O GLY o1425 " (cutoff:3.500A) Processing helix chain 'o' and resid 1434 through 1446 removed outlier: 3.588A pdb=" N VAL o1438 " --> pdb=" O GLU o1434 " (cutoff:3.500A) Processing helix chain 'o' and resid 1454 through 1459 Processing helix chain 'p' and resid 21 through 37 removed outlier: 4.342A pdb=" N TRP p 27 " --> pdb=" O GLN p 23 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ILE p 28 " --> pdb=" O GLU p 24 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL p 29 " --> pdb=" O ALA p 25 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N SER p 31 " --> pdb=" O TRP p 27 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER p 32 " --> pdb=" O ILE p 28 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLU p 36 " --> pdb=" O SER p 32 " (cutoff:3.500A) Processing helix chain 'p' and resid 40 through 53 removed outlier: 4.082A pdb=" N SER p 46 " --> pdb=" O GLN p 42 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE p 47 " --> pdb=" O GLN p 43 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP p 48 " --> pdb=" O LEU p 44 " (cutoff:3.500A) Processing helix chain 'p' and resid 55 through 61 removed outlier: 3.699A pdb=" N VAL p 59 " --> pdb=" O VAL p 55 " (cutoff:3.500A) Processing helix chain 'p' and resid 109 through 116 removed outlier: 3.567A pdb=" N ARG p 114 " --> pdb=" O PRO p 110 " (cutoff:3.500A) Processing helix chain 'p' and resid 167 through 172 Processing helix chain 'p' and resid 246 through 251 removed outlier: 4.140A pdb=" N ALA p 251 " --> pdb=" O ALA p 247 " (cutoff:3.500A) Processing helix chain 'p' and resid 269 through 275 Processing helix chain 'p' and resid 280 through 285 removed outlier: 3.818A pdb=" N LEU p 285 " --> pdb=" O ASP p 281 " (cutoff:3.500A) Processing helix chain 'p' and resid 294 through 302 removed outlier: 3.527A pdb=" N MET p 298 " --> pdb=" O ASP p 294 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N MET p 300 " --> pdb=" O GLU p 296 " (cutoff:3.500A) Processing helix chain 'p' and resid 303 through 309 removed outlier: 4.352A pdb=" N ASP p 306 " --> pdb=" O PRO p 303 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N GLU p 307 " --> pdb=" O SER p 304 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N PHE p 309 " --> pdb=" O ASP p 306 " (cutoff:3.500A) Processing helix chain 'p' and resid 313 through 323 Processing helix chain 'p' and resid 332 through 346 removed outlier: 3.656A pdb=" N LYS p 340 " --> pdb=" O ILE p 336 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLU p 341 " --> pdb=" O LYS p 337 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL p 342 " --> pdb=" O TYR p 338 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU p 343 " --> pdb=" O ALA p 339 " (cutoff:3.500A) Processing helix chain 'p' and resid 359 through 375 removed outlier: 3.511A pdb=" N LEU p 374 " --> pdb=" O HIS p 370 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA p 375 " --> pdb=" O ARG p 371 " (cutoff:3.500A) Processing helix chain 'p' and resid 387 through 389 No H-bonds generated for 'chain 'p' and resid 387 through 389' Processing helix chain 'p' and resid 396 through 424 removed outlier: 4.122A pdb=" N PHE p 402 " --> pdb=" O PRO p 398 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLY p 406 " --> pdb=" O PHE p 402 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N MET p 407 " --> pdb=" O LEU p 403 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ASN p 410 " --> pdb=" O GLY p 406 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU p 411 " --> pdb=" O MET p 407 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLU p 414 " --> pdb=" O ASN p 410 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL p 415 " --> pdb=" O LEU p 411 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG p 416 " --> pdb=" O LEU p 412 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ILE p 417 " --> pdb=" O LYS p 413 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N TYR p 418 " --> pdb=" O GLU p 414 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LYS p 421 " --> pdb=" O ILE p 417 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE p 422 " --> pdb=" O TYR p 418 " (cutoff:3.500A) Processing helix chain 'p' and resid 437 through 451 removed outlier: 3.792A pdb=" N SER p 441 " --> pdb=" O THR p 437 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASP p 442 " --> pdb=" O ARG p 438 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER p 447 " --> pdb=" O GLY p 443 " (cutoff:3.500A) Processing helix chain 'p' and resid 455 through 459 removed outlier: 3.696A pdb=" N ALA p 459 " --> pdb=" O GLN p 456 " (cutoff:3.500A) Processing helix chain 'p' and resid 474 through 480 removed outlier: 3.513A pdb=" N LEU p 479 " --> pdb=" O PHE p 475 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER p 480 " --> pdb=" O ALA p 476 " (cutoff:3.500A) Processing helix chain 'p' and resid 502 through 506 Processing helix chain 'p' and resid 538 through 548 Processing helix chain 'p' and resid 579 through 594 Processing helix chain 'p' and resid 636 through 641 removed outlier: 3.986A pdb=" N ILE p 640 " --> pdb=" O LYS p 636 " (cutoff:3.500A) Processing helix chain 'p' and resid 645 through 649 removed outlier: 3.840A pdb=" N ASN p 649 " --> pdb=" O ARG p 646 " (cutoff:3.500A) Processing helix chain 'p' and resid 653 through 658 Processing helix chain 'p' and resid 668 through 672 Processing helix chain 'p' and resid 678 through 683 Processing helix chain 'p' and resid 713 through 717 removed outlier: 3.554A pdb=" N HIS p 716 " --> pdb=" O PHE p 713 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ASN p 717 " --> pdb=" O PRO p 714 " (cutoff:3.500A) No H-bonds generated for 'chain 'p' and resid 713 through 717' Processing helix chain 'p' and resid 718 through 727 removed outlier: 3.799A pdb=" N ASN p 722 " --> pdb=" O GLN p 718 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR p 723 " --> pdb=" O SER p 719 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER p 726 " --> pdb=" O ASN p 722 " (cutoff:3.500A) Processing helix chain 'p' and resid 761 through 765 removed outlier: 4.042A pdb=" N GLU p 765 " --> pdb=" O ARG p 762 " (cutoff:3.500A) Processing helix chain 'p' and resid 798 through 802 Processing helix chain 'p' and resid 970 through 976 removed outlier: 4.564A pdb=" N SER p 974 " --> pdb=" O HIS p 970 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ARG p 975 " --> pdb=" O ALA p 971 " (cutoff:3.500A) Processing helix chain 'p' and resid 978 through 994 removed outlier: 3.507A pdb=" N GLU p 983 " --> pdb=" O GLY p 979 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N CYS p 984 " --> pdb=" O HIS p 980 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU p 985 " --> pdb=" O LEU p 981 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LYS p 988 " --> pdb=" O CYS p 984 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL p 989 " --> pdb=" O LEU p 985 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASN p 992 " --> pdb=" O LYS p 988 " (cutoff:3.500A) Processing helix chain 'p' and resid 1007 through 1019 removed outlier: 3.645A pdb=" N LEU p1014 " --> pdb=" O LYS p1010 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ASP p1017 " --> pdb=" O ASN p1013 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N TYR p1018 " --> pdb=" O LEU p1014 " (cutoff:3.500A) Processing helix chain 'p' and resid 1054 through 1058 removed outlier: 3.671A pdb=" N ASP p1057 " --> pdb=" O MET p1054 " (cutoff:3.500A) Processing helix chain 'p' and resid 1089 through 1098 removed outlier: 3.697A pdb=" N GLN p1094 " --> pdb=" O GLU p1090 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE p1095 " --> pdb=" O ARG p1091 " (cutoff:3.500A) Processing helix chain 'p' and resid 1099 through 1108 removed outlier: 3.627A pdb=" N LEU p1103 " --> pdb=" O ALA p1099 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU p1107 " --> pdb=" O LEU p1103 " (cutoff:3.500A) Processing helix chain 'p' and resid 1152 through 1164 removed outlier: 3.532A pdb=" N LYS p1156 " --> pdb=" O PRO p1152 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU p1158 " --> pdb=" O ALA p1154 " (cutoff:3.500A) Processing helix chain 'q' and resid 27 through 34 Processing helix chain 'q' and resid 60 through 70 removed outlier: 3.509A pdb=" N ILE q 64 " --> pdb=" O HIS q 60 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N HIS q 66 " --> pdb=" O GLU q 62 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLY q 69 " --> pdb=" O ALA q 65 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU q 70 " --> pdb=" O HIS q 66 " (cutoff:3.500A) Processing helix chain 'q' and resid 118 through 120 No H-bonds generated for 'chain 'q' and resid 118 through 120' Processing helix chain 'q' and resid 242 through 265 removed outlier: 3.503A pdb=" N LEU q 246 " --> pdb=" O GLU q 242 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LYS q 254 " --> pdb=" O SER q 250 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASP q 258 " --> pdb=" O LYS q 254 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N THR q 261 " --> pdb=" O SER q 257 " (cutoff:3.500A) Processing helix chain 'r' and resid 33 through 50 removed outlier: 3.505A pdb=" N LEU r 40 " --> pdb=" O GLU r 36 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLU r 42 " --> pdb=" O HIS r 38 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N HIS r 43 " --> pdb=" O MET r 39 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N SER r 50 " --> pdb=" O GLN r 46 " (cutoff:3.500A) Processing helix chain 'r' and resid 59 through 71 removed outlier: 3.702A pdb=" N ARG r 70 " --> pdb=" O ASN r 66 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE r 71 " --> pdb=" O TYR r 67 " (cutoff:3.500A) Processing helix chain 'r' and resid 76 through 87 removed outlier: 3.791A pdb=" N SER r 85 " --> pdb=" O ALA r 81 " (cutoff:3.500A) Processing helix chain 'r' and resid 93 through 102 removed outlier: 3.774A pdb=" N LEU r 97 " --> pdb=" O HIS r 93 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA r 98 " --> pdb=" O LYS r 94 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU r 100 " --> pdb=" O GLU r 96 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASN r 102 " --> pdb=" O ALA r 98 " (cutoff:3.500A) Processing helix chain 'r' and resid 107 through 115 Processing helix chain 'r' and resid 123 through 138 removed outlier: 4.055A pdb=" N LEU r 127 " --> pdb=" O GLU r 123 " (cutoff:3.500A) Processing helix chain 's' and resid 3 through 24 removed outlier: 3.561A pdb=" N TRP s 11 " --> pdb=" O THR s 7 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLN s 19 " --> pdb=" O LYS s 15 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N HIS s 22 " --> pdb=" O MET s 18 " (cutoff:3.500A) Processing helix chain 's' and resid 29 through 34 removed outlier: 3.901A pdb=" N LEU s 33 " --> pdb=" O THR s 29 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ASP s 34 " --> pdb=" O GLN s 30 " (cutoff:3.500A) No H-bonds generated for 'chain 's' and resid 29 through 34' Processing helix chain 's' and resid 36 through 44 Processing helix chain 's' and resid 84 through 98 Processing helix chain 's' and resid 111 through 119 removed outlier: 3.867A pdb=" N VAL s 119 " --> pdb=" O LYS s 115 " (cutoff:3.500A) Processing helix chain 's' and resid 133 through 137 removed outlier: 3.972A pdb=" N ILE s 137 " --> pdb=" O GLU s 134 " (cutoff:3.500A) Processing helix chain 's' and resid 138 through 142 removed outlier: 3.587A pdb=" N GLU s 141 " --> pdb=" O ASN s 138 " (cutoff:3.500A) Processing helix chain 's' and resid 155 through 163 removed outlier: 3.556A pdb=" N LEU s 160 " --> pdb=" O VAL s 156 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA s 161 " --> pdb=" O THR s 157 " (cutoff:3.500A) Processing helix chain 's' and resid 177 through 183 Processing helix chain 't' and resid 58 through 75 removed outlier: 3.680A pdb=" N ALA t 63 " --> pdb=" O LYS t 59 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY t 67 " --> pdb=" O ALA t 63 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N MET t 75 " --> pdb=" O LEU t 71 " (cutoff:3.500A) Processing helix chain 't' and resid 88 through 98 removed outlier: 3.823A pdb=" N ALA t 93 " --> pdb=" O PRO t 89 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N MET t 94 " --> pdb=" O LEU t 90 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS t 95 " --> pdb=" O LEU t 91 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU t 97 " --> pdb=" O ALA t 93 " (cutoff:3.500A) Processing helix chain 't' and resid 121 through 123 No H-bonds generated for 'chain 't' and resid 121 through 123' Processing helix chain 'w' and resid 63 through 67 Processing helix chain 'w' and resid 69 through 75 removed outlier: 3.714A pdb=" N VAL w 72 " --> pdb=" O ILE w 69 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N SER w 73 " --> pdb=" O ALA w 70 " (cutoff:3.500A) Processing helix chain 'x' and resid 17 through 28 removed outlier: 3.814A pdb=" N ALA x 27 " --> pdb=" O GLY x 23 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLU x 28 " --> pdb=" O LEU x 24 " (cutoff:3.500A) Processing helix chain 'x' and resid 30 through 35 Processing helix chain 'x' and resid 42 through 51 removed outlier: 3.642A pdb=" N ARG x 47 " --> pdb=" O TYR x 43 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N MET x 48 " --> pdb=" O CYS x 44 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N LEU x 49 " --> pdb=" O CYS x 45 " (cutoff:3.500A) Processing helix chain 'x' and resid 54 through 58 removed outlier: 3.904A pdb=" N GLU x 57 " --> pdb=" O ASP x 54 " (cutoff:3.500A) Processing helix chain 'y' and resid 5 through 10 removed outlier: 3.500A pdb=" N SER y 9 " --> pdb=" O ALA y 6 " (cutoff:3.500A) Processing helix chain 'y' and resid 39 through 51 removed outlier: 4.113A pdb=" N ILE y 45 " --> pdb=" O THR y 41 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE y 46 " --> pdb=" O LEU y 42 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS y 47 " --> pdb=" O GLY y 43 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLN y 49 " --> pdb=" O ILE y 45 " (cutoff:3.500A) Processing helix chain 'y' and resid 82 through 110 removed outlier: 3.558A pdb=" N ASP y 93 " --> pdb=" O ASN y 89 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU y 100 " --> pdb=" O SER y 96 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS y 110 " --> pdb=" O ARG y 106 " (cutoff:3.500A) Processing helix chain 'y' and resid 111 through 113 No H-bonds generated for 'chain 'y' and resid 111 through 113' Processing helix chain 'u' and resid 14 through 18 removed outlier: 3.792A pdb=" N PHE u 18 " --> pdb=" O PRO u 15 " (cutoff:3.500A) Processing helix chain 'u' and resid 21 through 33 removed outlier: 3.661A pdb=" N THR u 25 " --> pdb=" O ASN u 21 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS u 27 " --> pdb=" O LEU u 23 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR u 32 " --> pdb=" O GLN u 28 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N GLU u 33 " --> pdb=" O LYS u 29 " (cutoff:3.500A) Processing helix chain 'u' and resid 111 through 113 No H-bonds generated for 'chain 'u' and resid 111 through 113' Processing sheet with id=AA1, first strand: chain 'A' and resid 786 through 787 removed outlier: 7.756A pdb=" N LEU A 678 " --> pdb=" O ASP A 778 " (cutoff:3.500A) removed outlier: 8.920A pdb=" N PHE A 780 " --> pdb=" O LEU A 678 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LEU A 680 " --> pdb=" O PHE A 780 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N VAL A 782 " --> pdb=" O LEU A 680 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N GLU A 682 " --> pdb=" O VAL A 782 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASP A 677 " --> pdb=" O THR G 79 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR G 79 " --> pdb=" O ASP A 677 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N VAL G 73 " --> pdb=" O TYR A 683 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N LEU G 43 " --> pdb=" O VAL A 636 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N TYR A 771 " --> pdb=" O SER A 635 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ARG A 766 " --> pdb=" O SER G 14 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N SER G 14 " --> pdb=" O ARG A 766 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N GLN G 15 " --> pdb=" O GLN G 93 " (cutoff:3.500A) removed outlier: 8.801A pdb=" N LEU G 95 " --> pdb=" O GLN G 15 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N ILE G 17 " --> pdb=" O LEU G 95 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N SER G 97 " --> pdb=" O ILE G 17 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ARG G 19 " --> pdb=" O SER G 97 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 786 through 787 removed outlier: 7.756A pdb=" N LEU A 678 " --> pdb=" O ASP A 778 " (cutoff:3.500A) removed outlier: 8.920A pdb=" N PHE A 780 " --> pdb=" O LEU A 678 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LEU A 680 " --> pdb=" O PHE A 780 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N VAL A 782 " --> pdb=" O LEU A 680 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N GLU A 682 " --> pdb=" O VAL A 782 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASP A 677 " --> pdb=" O THR G 79 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR G 79 " --> pdb=" O ASP A 677 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N VAL G 73 " --> pdb=" O TYR A 683 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N LYS G 66 " --> pdb=" O THR G 98 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N THR G 98 " --> pdb=" O LYS G 66 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N VAL G 68 " --> pdb=" O VAL G 96 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N VAL G 96 " --> pdb=" O VAL G 68 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N LEU G 70 " --> pdb=" O MET G 94 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N MET G 94 " --> pdb=" O LEU G 70 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N CYS G 72 " --> pdb=" O CYS G 92 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N CYS G 92 " --> pdb=" O CYS G 72 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N MET G 74 " --> pdb=" O ASP G 90 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ASP G 90 " --> pdb=" O MET G 74 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N SER G 76 " --> pdb=" O THR G 88 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 786 through 787 removed outlier: 4.292A pdb=" N GLN A 741 " --> pdb=" O ILE A 752 " (cutoff:3.500A) removed outlier: 9.008A pdb=" N LEU A 754 " --> pdb=" O LEU A 739 " (cutoff:3.500A) removed outlier: 12.851A pdb=" N LEU A 739 " --> pdb=" O LEU A 754 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 824 through 825 Processing sheet with id=AA5, first strand: chain 'A' and resid 947 through 948 Processing sheet with id=AA6, first strand: chain 'A' and resid 1165 through 1167 Processing sheet with id=AA7, first strand: chain 'B' and resid 80 through 81 removed outlier: 5.553A pdb=" N ILE B 72 " --> pdb=" O SER B 151 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N SER B 151 " --> pdb=" O ILE B 72 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG B 74 " --> pdb=" O ASN B 149 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N VAL B 46 " --> pdb=" O ASN B 37 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N ASN B 37 " --> pdb=" O VAL B 46 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N PHE B 48 " --> pdb=" O ILE B 35 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N ILE B 35 " --> pdb=" O PHE B 48 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N GLU B 50 " --> pdb=" O VAL B 33 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N VAL B 33 " --> pdb=" O GLU B 50 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N THR B 52 " --> pdb=" O GLN B 31 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N GLN B 31 " --> pdb=" O THR B 52 " (cutoff:3.500A) removed outlier: 8.768A pdb=" N PHE B 54 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N THR B 29 " --> pdb=" O PHE B 54 " (cutoff:3.500A) removed outlier: 9.633A pdb=" N THR B 201 " --> pdb=" O LYS B 27 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N THR B 29 " --> pdb=" O THR B 201 " (cutoff:3.500A) removed outlier: 8.364A pdb=" N LYS B 203 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N GLN B 31 " --> pdb=" O LYS B 203 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N GLU B 205 " --> pdb=" O GLN B 31 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N VAL B 33 " --> pdb=" O GLU B 205 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N THR B 207 " --> pdb=" O VAL B 33 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N ILE B 35 " --> pdb=" O THR B 207 " (cutoff:3.500A) removed outlier: 8.867A pdb=" N ASP B 209 " --> pdb=" O ILE B 35 " (cutoff:3.500A) removed outlier: 10.419A pdb=" N ASN B 37 " --> pdb=" O ASP B 209 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N CYS B 200 " --> pdb=" O ILE B 240 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ILE B 240 " --> pdb=" O CYS B 200 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU B 222 " --> pdb=" O HIS B 235 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N MET B 237 " --> pdb=" O LEU B 220 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N LEU B 220 " --> pdb=" O MET B 237 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 63 through 65 removed outlier: 4.057A pdb=" N ALA B 83 " --> pdb=" O LYS B 129 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 159 through 162 removed outlier: 5.757A pdb=" N LEU B 249 " --> pdb=" O SER B 179 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 255 through 258 removed outlier: 6.356A pdb=" N LYS B 305 " --> pdb=" O SER B 323 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N PHE B 325 " --> pdb=" O LYS B 305 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N VAL B 307 " --> pdb=" O PHE B 325 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N MET B 322 " --> pdb=" O TYR B 319 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 360 through 361 removed outlier: 6.562A pdb=" N SER B 360 " --> pdb=" O VAL B 498 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 587 through 591 removed outlier: 4.570A pdb=" N PHE B 535 " --> pdb=" O GLU B 643 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 573 through 580 removed outlier: 7.405A pdb=" N LYS B 565 " --> pdb=" O ILE B 630 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N ILE B 630 " --> pdb=" O LYS B 565 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N THR B 567 " --> pdb=" O ILE B 628 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ILE B 628 " --> pdb=" O THR B 567 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N GLN B 569 " --> pdb=" O LEU B 626 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 604 through 605 Processing sheet with id=AB6, first strand: chain 'D' and resid 934 through 935 Processing sheet with id=AB7, first strand: chain 'E' and resid 308 through 310 Processing sheet with id=AB8, first strand: chain 'E' and resid 782 through 785 Processing sheet with id=AB9, first strand: chain 'E' and resid 473 through 478 removed outlier: 3.999A pdb=" N THR E 493 " --> pdb=" O PHE E 489 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 504 through 507 removed outlier: 3.718A pdb=" N SER E 506 " --> pdb=" O THR E 532 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N THR E 532 " --> pdb=" O SER E 506 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 546 through 550 removed outlier: 3.506A pdb=" N SER E 562 " --> pdb=" O THR E 566 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N THR E 566 " --> pdb=" O SER E 562 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL E 579 " --> pdb=" O LEU E 569 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 588 through 593 Processing sheet with id=AC4, first strand: chain 'E' and resid 634 through 635 removed outlier: 3.617A pdb=" N ARG E 663 " --> pdb=" O LEU E 653 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ASP E 655 " --> pdb=" O CYS E 661 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N CYS E 661 " --> pdb=" O ASP E 655 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 672 through 677 Processing sheet with id=AC6, first strand: chain 'E' and resid 714 through 719 removed outlier: 6.477A pdb=" N LEU E 737 " --> pdb=" O LEU E 770 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 86 through 88 Processing sheet with id=AC8, first strand: chain 'H' and resid 200 through 201 Processing sheet with id=AC9, first strand: chain 'O' and resid 67 through 68 removed outlier: 3.901A pdb=" N ASN Q 333 " --> pdb=" O LYS O 92 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N VAL Q 334 " --> pdb=" O MET Q 358 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N MET Q 358 " --> pdb=" O VAL Q 334 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N VAL Q 336 " --> pdb=" O GLY Q 356 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N GLY Q 356 " --> pdb=" O VAL Q 336 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N HIS Q 352 " --> pdb=" O ASP Q 340 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ILE Q 342 " --> pdb=" O LYS Q 350 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N LYS Q 350 " --> pdb=" O ILE Q 342 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ARG Q 344 " --> pdb=" O LYS Q 348 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N LYS Q 348 " --> pdb=" O ARG Q 344 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N LYS Q 348 " --> pdb=" O GLU Q 375 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N GLU Q 375 " --> pdb=" O LYS Q 348 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N LYS Q 350 " --> pdb=" O ASP Q 373 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ASP Q 373 " --> pdb=" O LYS Q 350 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N HIS Q 352 " --> pdb=" O ILE Q 371 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N ILE Q 371 " --> pdb=" O HIS Q 352 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N LYS Q 354 " --> pdb=" O LYS Q 369 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N LYS Q 369 " --> pdb=" O LYS Q 354 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLU Q 375 " --> pdb=" O GLY O 60 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU O 62 " --> pdb=" O GLU Q 375 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N SER O 61 " --> pdb=" O ASN O 77 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N VAL O 75 " --> pdb=" O ASN O 63 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'O' and resid 81 through 83 Processing sheet with id=AD2, first strand: chain 'P' and resid 190 through 191 removed outlier: 3.837A pdb=" N THR P 209 " --> pdb=" O ILE P 204 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLY P 223 " --> pdb=" O ILE P 168 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N ILE P 168 " --> pdb=" O GLY P 223 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N VAL P 259 " --> pdb=" O GLN P 166 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N ILE P 168 " --> pdb=" O ASN P 257 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ASN P 257 " --> pdb=" O ILE P 168 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N SER P 170 " --> pdb=" O ILE P 255 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ILE P 255 " --> pdb=" O SER P 170 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N VAL P 172 " --> pdb=" O PHE P 253 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N PHE P 253 " --> pdb=" O VAL P 172 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N MET P 258 " --> pdb=" O GLY P 314 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLY P 314 " --> pdb=" O MET P 258 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'R' and resid 24 through 26 Processing sheet with id=AD4, first strand: chain 'S' and resid 45 through 49 removed outlier: 3.861A pdb=" N ASN S 142 " --> pdb=" O TYR S 26 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA S 30 " --> pdb=" O TYR S 144 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N ASN S 32 " --> pdb=" O PHE S 146 " (cutoff:3.500A) removed outlier: 11.722A pdb=" N GLN T 91 " --> pdb=" O VAL T 111 " (cutoff:3.500A) removed outlier: 8.840A pdb=" N VAL T 111 " --> pdb=" O GLN T 91 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N LEU T 93 " --> pdb=" O ILE T 109 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N ILE T 109 " --> pdb=" O LEU T 93 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N VAL T 95 " --> pdb=" O GLU T 107 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N VAL T 18 " --> pdb=" O VAL T 110 " (cutoff:3.500A) removed outlier: 8.557A pdb=" N GLY T 17 " --> pdb=" O GLN S 129 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N GLN S 129 " --> pdb=" O GLY T 17 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N PHE S 135 " --> pdb=" O GLU S 13 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N VAL S 15 " --> pdb=" O PHE S 135 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N ALA S 137 " --> pdb=" O VAL S 15 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ARG S 17 " --> pdb=" O ALA S 137 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG T 51 " --> pdb=" O THR T 48 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'T' and resid 7 through 8 removed outlier: 3.814A pdb=" N ARG T 113 " --> pdb=" O GLN T 86 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'f' and resid 111 through 113 removed outlier: 8.243A pdb=" N SER c 25 " --> pdb=" O LEU j 195 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'd' and resid 893 through 894 removed outlier: 7.793A pdb=" N GLU d 893 " --> pdb=" O LEU l 111 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'd' and resid 934 through 936 Processing sheet with id=AD9, first strand: chain 'e' and resid 461 through 466 removed outlier: 6.412A pdb=" N ILE e 461 " --> pdb=" O LEU f 136 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'e' and resid 473 through 478 removed outlier: 3.852A pdb=" N THR e 493 " --> pdb=" O PHE e 489 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'e' and resid 506 through 507 removed outlier: 4.285A pdb=" N SER e 506 " --> pdb=" O ASP e 529 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'e' and resid 546 through 550 removed outlier: 6.692A pdb=" N SER e 561 " --> pdb=" O TYR e 547 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ALA e 549 " --> pdb=" O LEU e 559 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N LEU e 559 " --> pdb=" O ALA e 549 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL e 579 " --> pdb=" O LEU e 569 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'e' and resid 588 through 593 Processing sheet with id=AE5, first strand: chain 'e' and resid 632 through 635 removed outlier: 3.635A pdb=" N ARG e 652 " --> pdb=" O THR e 644 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG e 663 " --> pdb=" O LEU e 653 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ASP e 655 " --> pdb=" O CYS e 661 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N CYS e 661 " --> pdb=" O ASP e 655 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'e' and resid 672 through 677 removed outlier: 6.680A pdb=" N GLY e 687 " --> pdb=" O HIS e 673 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N LEU e 675 " --> pdb=" O ALA e 685 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ALA e 685 " --> pdb=" O LEU e 675 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N PHE e 677 " --> pdb=" O PHE e 683 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N PHE e 683 " --> pdb=" O PHE e 677 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ASP e 697 " --> pdb=" O MET e 703 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N MET e 703 " --> pdb=" O ASP e 697 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'e' and resid 716 through 719 Processing sheet with id=AE8, first strand: chain 'e' and resid 782 through 785 removed outlier: 4.238A pdb=" N HIS e 782 " --> pdb=" O ALA e 794 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA e 794 " --> pdb=" O HIS e 782 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'f' and resid 95 through 97 removed outlier: 3.504A pdb=" N LEU f 104 " --> pdb=" O ALA f 97 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'o' and resid 86 through 94 removed outlier: 3.732A pdb=" N LEU o 90 " --> pdb=" O THR o 251 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N THR o 251 " --> pdb=" O LEU o 90 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'o' and resid 190 through 191 removed outlier: 3.773A pdb=" N GLU o 201 " --> pdb=" O ARG o 190 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'o' and resid 264 through 266 removed outlier: 3.842A pdb=" N MET o 266 " --> pdb=" O ALA o 270 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ALA o 270 " --> pdb=" O MET o 266 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'o' and resid 357 through 358 removed outlier: 4.375A pdb=" N LYS o 357 " --> pdb=" O PHE p1086 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'p' and resid 1060 through 1062 removed outlier: 3.765A pdb=" N THR o 365 " --> pdb=" O MET o 501 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL o 456 " --> pdb=" O HIS o 472 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N PHE o 482 " --> pdb=" O ARG o 364 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N VAL o 366 " --> pdb=" O PHE o 482 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N LEU o 484 " --> pdb=" O VAL o 366 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N THR o 368 " --> pdb=" O LEU o 484 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'o' and resid 389 through 393 removed outlier: 4.151A pdb=" N TYR o 418 " --> pdb=" O GLU o 447 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N HIS o 449 " --> pdb=" O ALA o 416 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N ALA o 416 " --> pdb=" O HIS o 449 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'o' and resid 526 through 527 removed outlier: 3.813A pdb=" N ARG o 532 " --> pdb=" O THR o 527 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'o' and resid 554 through 555 Processing sheet with id=AF9, first strand: chain 'o' and resid 602 through 603 removed outlier: 6.845A pdb=" N VAL o 629 " --> pdb=" O ILE o 636 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'o' and resid 685 through 686 removed outlier: 3.833A pdb=" N HIS o 685 " --> pdb=" O SER p 784 " (cutoff:3.500A) removed outlier: 8.968A pdb=" N ILE p 965 " --> pdb=" O ASN p 777 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ILE p 779 " --> pdb=" O ILE p 965 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N ILE p 967 " --> pdb=" O ILE p 779 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ALA p 781 " --> pdb=" O ILE p 967 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N VAL p 794 " --> pdb=" O GLY p 946 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N GLN p 948 " --> pdb=" O VAL p 794 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N MET p 796 " --> pdb=" O GLN p 948 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'o' and resid 685 through 686 removed outlier: 3.833A pdb=" N HIS o 685 " --> pdb=" O SER p 784 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N PHE p1042 " --> pdb=" O ILE p 782 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'o' and resid 789 through 790 Processing sheet with id=AG4, first strand: chain 'o' and resid 872 through 873 removed outlier: 6.936A pdb=" N VAL o 879 " --> pdb=" O VAL o 887 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'o' and resid 902 through 905 Processing sheet with id=AG6, first strand: chain 'o' and resid 1140 through 1142 Processing sheet with id=AG7, first strand: chain 'o' and resid 1243 through 1247 removed outlier: 4.269A pdb=" N LEU o1255 " --> pdb=" O LEU o1216 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU o1211 " --> pdb=" O ILE o1175 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N ILE o1175 " --> pdb=" O LEU o1211 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ARG o1213 " --> pdb=" O THR o1173 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N THR o1173 " --> pdb=" O ARG o1213 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLU o1215 " --> pdb=" O ALA o1171 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'o' and resid 1319 through 1322 Processing sheet with id=AG9, first strand: chain 't' and resid 115 through 119 removed outlier: 3.537A pdb=" N ASP o1472 " --> pdb=" O ARG t 107 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N LEU o1473 " --> pdb=" O ILE u 59 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE u 59 " --> pdb=" O LEU o1473 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLY u 57 " --> pdb=" O LEU o1475 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL u 66 " --> pdb=" O LEU u 13 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE u 5 " --> pdb=" O ALA u 74 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 't' and resid 115 through 119 removed outlier: 3.537A pdb=" N ASP o1472 " --> pdb=" O ARG t 107 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N LEU o1473 " --> pdb=" O ILE u 59 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE u 59 " --> pdb=" O LEU o1473 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLY u 57 " --> pdb=" O LEU o1475 " (cutoff:3.500A) removed outlier: 11.235A pdb=" N LEU u 67 " --> pdb=" O ILE u 54 " (cutoff:3.500A) removed outlier: 10.343A pdb=" N ILE u 54 " --> pdb=" O LEU u 67 " (cutoff:3.500A) removed outlier: 8.831A pdb=" N ASP u 52 " --> pdb=" O PRO u 69 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N LYS u 71 " --> pdb=" O THR u 50 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N THR u 50 " --> pdb=" O LYS u 71 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N LYS u 73 " --> pdb=" O VAL u 48 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N VAL u 48 " --> pdb=" O LYS u 73 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N ILE u 75 " --> pdb=" O ILE u 46 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE u 46 " --> pdb=" O ILE u 75 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'p' and resid 83 through 84 removed outlier: 4.861A pdb=" N LEU p 93 " --> pdb=" O PRO p 123 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N TYR p 125 " --> pdb=" O ILE p 91 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N ILE p 91 " --> pdb=" O TYR p 125 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ASP p 127 " --> pdb=" O GLU p 89 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'p' and resid 83 through 84 removed outlier: 6.603A pdb=" N ALA p 122 " --> pdb=" O GLY p 150 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N GLY p 150 " --> pdb=" O ALA p 122 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N LEU p 124 " --> pdb=" O PHE p 148 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N PHE p 148 " --> pdb=" O LEU p 124 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N VAL p 126 " --> pdb=" O LYS p 146 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU p 140 " --> pdb=" O VAL p 132 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'p' and resid 97 through 99 Processing sheet with id=AH5, first strand: chain 'p' and resid 185 through 187 Processing sheet with id=AH6, first strand: chain 'p' and resid 391 through 394 removed outlier: 3.560A pdb=" N LYS p 524 " --> pdb=" O LEU p 485 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'p' and resid 206 through 208 removed outlier: 6.851A pdb=" N MET p 239 " --> pdb=" O ALA p 216 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N THR p 218 " --> pdb=" O VAL p 237 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N VAL p 237 " --> pdb=" O THR p 218 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N GLU p 220 " --> pdb=" O ILE p 235 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ILE p 235 " --> pdb=" O GLU p 220 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N ARG p 222 " --> pdb=" O SER p 233 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N SER p 233 " --> pdb=" O ARG p 222 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N TRP p 236 " --> pdb=" O THR p 259 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'p' and resid 531 through 532 Processing sheet with id=AH9, first strand: chain 'p' and resid 572 through 573 removed outlier: 3.548A pdb=" N ILE p 614 " --> pdb=" O PHE p 568 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU p 611 " --> pdb=" O ASP p 606 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASP p 606 " --> pdb=" O GLU p 611 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER p 602 " --> pdb=" O TYR p 615 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'p' and resid 662 through 664 Processing sheet with id=AI2, first strand: chain 'p' and resid 748 through 751 removed outlier: 3.564A pdb=" N VAL p 750 " --> pdb=" O VAL p 809 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N PHE p 918 " --> pdb=" O VAL p 909 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N VAL p 909 " --> pdb=" O PHE p 918 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N LYS p 920 " --> pdb=" O VAL p 907 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N VAL p 907 " --> pdb=" O LYS p 920 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ARG p 922 " --> pdb=" O ASP p 905 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N VAL p 907 " --> pdb=" O LYS z 46 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'p' and resid 759 through 760 removed outlier: 3.517A pdb=" N THR p 760 " --> pdb=" O GLY p 997 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI3 Processing sheet with id=AI4, first strand: chain 'p' and resid 827 through 829 removed outlier: 3.916A pdb=" N ILE p 867 " --> pdb=" O THR p 894 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'p' and resid 1115 through 1119 Processing sheet with id=AI6, first strand: chain 'p' and resid 1127 through 1129 Processing sheet with id=AI7, first strand: chain 'q' and resid 8 through 14 removed outlier: 6.522A pdb=" N LYS q 20 " --> pdb=" O THR q 12 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N LEU q 14 " --> pdb=" O ASN q 18 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ASN q 18 " --> pdb=" O LEU q 14 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N PHE q 21 " --> pdb=" O TYR q 231 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'q' and resid 121 through 122 removed outlier: 3.517A pdb=" N ALA q 163 " --> pdb=" O PHE q 101 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N GLU q 158 " --> pdb=" O ALA q 54 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ALA q 54 " --> pdb=" O GLU q 158 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N ARG q 160 " --> pdb=" O ILE q 52 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N ILE q 52 " --> pdb=" O ARG q 160 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ARG q 162 " --> pdb=" O VAL q 50 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N VAL q 50 " --> pdb=" O ARG q 162 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N TYR q 164 " --> pdb=" O ASP q 48 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'q' and resid 113 through 116 removed outlier: 3.642A pdb=" N VAL q 151 " --> pdb=" O VAL q 115 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 's' and resid 60 through 63 removed outlier: 3.752A pdb=" N VAL s 60 " --> pdb=" O VAL s 74 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ARG s 101 " --> pdb=" O GLN s 71 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 's' and resid 81 through 82 Processing sheet with id=AJ3, first strand: chain 's' and resid 147 through 150 removed outlier: 3.805A pdb=" N GLU s 147 " --> pdb=" O ILE s 194 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 't' and resid 56 through 57 Processing sheet with id=AJ5, first strand: chain 'v' and resid 4 through 14 removed outlier: 6.910A pdb=" N HIS v 29 " --> pdb=" O LYS v 13 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N LEU v 122 " --> pdb=" O ASP v 42 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY v 127 " --> pdb=" O LEU v 112 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N SER v 113 " --> pdb=" O GLU v 100 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ARG v 98 " --> pdb=" O TYR v 115 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N SER v 117 " --> pdb=" O VAL v 96 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N VAL v 96 " --> pdb=" O SER v 117 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'w' and resid 25 through 28 Processing sheet with id=AJ7, first strand: chain 'w' and resid 80 through 81 Processing sheet with id=AJ8, first strand: chain 'y' and resid 21 through 23 removed outlier: 6.629A pdb=" N ILE y 72 " --> pdb=" O TYR y 61 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N TYR y 61 " --> pdb=" O ILE y 72 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ARG y 74 " --> pdb=" O ALA y 59 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ALA y 59 " --> pdb=" O ARG y 74 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N GLN y 76 " --> pdb=" O LEU y 57 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'u' and resid 169 through 170 removed outlier: 3.666A pdb=" N LYS u 146 " --> pdb=" O SER u 162 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ILE u 160 " --> pdb=" O VAL u 148 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N THR u 150 " --> pdb=" O PHE u 158 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N PHE u 158 " --> pdb=" O THR u 150 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N VAL u 152 " --> pdb=" O ASP u 156 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ASP u 156 " --> pdb=" O VAL u 152 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N SER u 105 " --> pdb=" O ALA u 159 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N GLY u 161 " --> pdb=" O SER u 105 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N PHE u 107 " --> pdb=" O GLY u 161 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N GLY u 96 " --> pdb=" O VAL u 92 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N VAL u 92 " --> pdb=" O GLY u 96 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N PHE u 98 " --> pdb=" O THR u 90 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'u' and resid 118 through 120 3045 hydrogen bonds defined for protein. 8628 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 144 hydrogen bonds 280 hydrogen bond angles 0 basepair planarities 58 basepair parallelities 141 stacking parallelities Total time for adding SS restraints: 38.70 Time building geometry restraints manager: 26.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 13397 1.31 - 1.45: 22706 1.45 - 1.58: 46623 1.58 - 1.72: 306 1.72 - 1.85: 718 Bond restraints: 83750 Sorted by residual: bond pdb=" CA GLU o 715 " pdb=" C GLU o 715 " ideal model delta sigma weight residual 1.523 1.435 0.089 1.30e-02 5.92e+03 4.65e+01 bond pdb=" C GLN D1001 " pdb=" O GLN D1001 " ideal model delta sigma weight residual 1.236 1.321 -0.085 1.29e-02 6.01e+03 4.32e+01 bond pdb=" CA ILE o 702 " pdb=" CB ILE o 702 " ideal model delta sigma weight residual 1.540 1.461 0.079 1.25e-02 6.40e+03 4.03e+01 bond pdb=" C ASN B 61 " pdb=" O ASN B 61 " ideal model delta sigma weight residual 1.239 1.179 0.059 9.60e-03 1.09e+04 3.83e+01 bond pdb=" CA ILE o 706 " pdb=" CB ILE o 706 " ideal model delta sigma weight residual 1.540 1.471 0.070 1.25e-02 6.40e+03 3.10e+01 ... (remaining 83745 not shown) Histogram of bond angle deviations from ideal: 95.85 - 104.39: 2009 104.39 - 112.93: 44801 112.93 - 121.46: 47056 121.46 - 130.00: 19470 130.00 - 138.54: 562 Bond angle restraints: 113898 Sorted by residual: angle pdb=" C ARG P 203 " pdb=" CA ARG P 203 " pdb=" CB ARG P 203 " ideal model delta sigma weight residual 111.22 130.65 -19.43 2.02e+00 2.45e-01 9.25e+01 angle pdb=" O PRO f 149 " pdb=" C PRO f 149 " pdb=" N PRO f 150 " ideal model delta sigma weight residual 121.31 125.55 -4.24 4.60e-01 4.73e+00 8.48e+01 angle pdb=" N ARG R 112 " pdb=" CA ARG R 112 " pdb=" C ARG R 112 " ideal model delta sigma weight residual 111.28 101.24 10.04 1.09e+00 8.42e-01 8.48e+01 angle pdb=" C MET P 202 " pdb=" N ARG P 203 " pdb=" CA ARG P 203 " ideal model delta sigma weight residual 123.32 107.34 15.98 1.88e+00 2.83e-01 7.22e+01 angle pdb=" N THR o 736 " pdb=" CA THR o 736 " pdb=" C THR o 736 " ideal model delta sigma weight residual 111.11 101.27 9.84 1.20e+00 6.94e-01 6.72e+01 ... (remaining 113893 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.47: 48668 34.47 - 68.94: 1973 68.94 - 103.41: 82 103.41 - 137.88: 1 137.88 - 172.35: 1 Dihedral angle restraints: 50725 sinusoidal: 21929 harmonic: 28796 Sorted by residual: dihedral pdb=" CA ARG A 821 " pdb=" C ARG A 821 " pdb=" N PRO A 822 " pdb=" CA PRO A 822 " ideal model delta harmonic sigma weight residual 180.00 69.94 110.06 0 5.00e+00 4.00e-02 4.85e+02 dihedral pdb=" C ARG P 203 " pdb=" N ARG P 203 " pdb=" CA ARG P 203 " pdb=" CB ARG P 203 " ideal model delta harmonic sigma weight residual -122.60 -147.90 25.30 0 2.50e+00 1.60e-01 1.02e+02 dihedral pdb=" N ARG P 203 " pdb=" C ARG P 203 " pdb=" CA ARG P 203 " pdb=" CB ARG P 203 " ideal model delta harmonic sigma weight residual 122.80 139.53 -16.73 0 2.50e+00 1.60e-01 4.48e+01 ... (remaining 50722 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.175: 12270 0.175 - 0.350: 409 0.350 - 0.526: 27 0.526 - 0.701: 2 0.701 - 0.876: 1 Chirality restraints: 12709 Sorted by residual: chirality pdb=" CA ARG P 203 " pdb=" N ARG P 203 " pdb=" C ARG P 203 " pdb=" CB ARG P 203 " both_signs ideal model delta sigma weight residual False 2.51 1.63 0.88 2.00e-01 2.50e+01 1.92e+01 chirality pdb=" CA THR o 705 " pdb=" N THR o 705 " pdb=" C THR o 705 " pdb=" CB THR o 705 " both_signs ideal model delta sigma weight residual False 2.53 1.88 0.65 2.00e-01 2.50e+01 1.05e+01 chirality pdb=" CA ARG F 268 " pdb=" N ARG F 268 " pdb=" C ARG F 268 " pdb=" CB ARG F 268 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.54 2.00e-01 2.50e+01 7.21e+00 ... (remaining 12706 not shown) Planarity restraints: 14167 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR p1000 " -0.031 2.00e-02 2.50e+03 6.05e-02 3.66e+01 pdb=" C THR p1000 " 0.105 2.00e-02 2.50e+03 pdb=" O THR p1000 " -0.039 2.00e-02 2.50e+03 pdb=" N PRO p1001 " -0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 969 " 0.028 2.00e-02 2.50e+03 5.72e-02 3.27e+01 pdb=" C PRO A 969 " -0.099 2.00e-02 2.50e+03 pdb=" O PRO A 969 " 0.038 2.00e-02 2.50e+03 pdb=" N ASN A 970 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS F 389 " -0.026 2.00e-02 2.50e+03 5.21e-02 2.71e+01 pdb=" C LYS F 389 " 0.090 2.00e-02 2.50e+03 pdb=" O LYS F 389 " -0.033 2.00e-02 2.50e+03 pdb=" N THR F 390 " -0.031 2.00e-02 2.50e+03 ... (remaining 14164 not shown) Histogram of nonbonded interaction distances: 1.50 - 2.18: 110 2.18 - 2.86: 28983 2.86 - 3.54: 107491 3.54 - 4.22: 194091 4.22 - 4.90: 326587 Nonbonded interactions: 657262 Sorted by model distance: nonbonded pdb=" NH1 ARG l 106 " pdb=" NZ LYS l 114 " model vdw 1.497 3.200 nonbonded pdb=" O LEU D1006 " pdb=" CG ASP Q 330 " model vdw 1.534 3.270 nonbonded pdb=" O ASN T 123 " pdb=" N MET T 125 " model vdw 1.539 2.520 nonbonded pdb=" CB ALA S 160 " pdb=" CB VAL p 310 " model vdw 1.539 3.890 nonbonded pdb=" OE2 GLU P 271 " pdb=" CD1 LEU R 208 " model vdw 1.578 3.460 ... (remaining 657257 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'E' and (resid 209 through 343 or resid 363 through 798)) selection = (chain 'e' and (resid 209 through 378 or resid 417 through 747 or resid 754 thro \ ugh 798)) } ncs_group { reference = (chain 'F' and (resid 14 through 150 or resid 210 or resid 214 through 473)) selection = (chain 'f' and (resid 14 through 106 or (resid 107 through 108 and (name N or na \ me CA or name C or name O or name CB )) or resid 109 through 123 or (resid 124 a \ nd (name N or name CA or name C or name O or name CB )) or resid 125 through 473 \ )) } ncs_group { reference = chain 'I' selection = (chain 'i' and resid 13 through 132) } ncs_group { reference = chain 'J' selection = (chain 'j' and (resid 114 through 177 or resid 192 through 216)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.090 Extract box with map and model: 24.940 Check model and map are aligned: 0.880 Set scattering table: 0.590 Process input model: 190.320 Find NCS groups from input model: 2.320 Set up NCS constraints: 0.290 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 226.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3534 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.121 83750 Z= 0.499 Angle : 1.085 19.427 113898 Z= 0.718 Chirality : 0.073 0.876 12709 Planarity : 0.006 0.105 14167 Dihedral : 16.724 172.350 32032 Min Nonbonded Distance : 1.497 Molprobity Statistics. All-atom Clashscore : 20.97 Ramachandran Plot: Outliers : 0.47 % Allowed : 6.11 % Favored : 93.42 % Rotamer: Outliers : 3.31 % Allowed : 6.97 % Favored : 89.73 % Cbeta Deviations : 0.36 % Peptide Plane: Cis-proline : 0.42 % Cis-general : 0.00 % Twisted Proline : 0.21 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.70 (0.07), residues: 9695 helix: -2.70 (0.07), residues: 3797 sheet: -1.59 (0.14), residues: 1265 loop : -2.43 (0.08), residues: 4633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.084 0.003 TRP T 19 HIS 0.015 0.001 HIS F 385 PHE 0.035 0.002 PHE B 190 TYR 0.036 0.002 TYR p1048 ARG 0.049 0.001 ARG u 144 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19390 Ramachandran restraints generated. 9695 Oldfield, 0 Emsley, 9695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19390 Ramachandran restraints generated. 9695 Oldfield, 0 Emsley, 9695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1344 residues out of total 8741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 286 poor density : 1058 time to evaluate : 7.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 665 MET cc_start: -0.3130 (mmm) cc_final: -0.3977 (mtt) REVERT: A 711 ASP cc_start: 0.2137 (OUTLIER) cc_final: 0.1583 (t70) REVERT: A 1165 LEU cc_start: -0.2143 (OUTLIER) cc_final: -0.3248 (tt) REVERT: B 619 MET cc_start: -0.3299 (ttp) cc_final: -0.3611 (ttt) REVERT: E 703 MET cc_start: -0.1730 (ptm) cc_final: -0.1936 (ptm) REVERT: F 63 ARG cc_start: 0.0646 (OUTLIER) cc_final: -0.0266 (ptp-170) REVERT: G 184 ILE cc_start: -0.2915 (OUTLIER) cc_final: -0.3617 (tt) REVERT: O 76 LEU cc_start: 0.6663 (OUTLIER) cc_final: 0.6336 (mm) REVERT: Q 317 GLU cc_start: -0.2825 (OUTLIER) cc_final: -0.4657 (mm-30) REVERT: Q 318 ASP cc_start: 0.4497 (OUTLIER) cc_final: 0.3873 (p0) REVERT: c 73 MET cc_start: 0.0652 (mmm) cc_final: 0.0338 (mmt) REVERT: d 888 LYS cc_start: -0.2343 (OUTLIER) cc_final: -0.3157 (pttt) REVERT: e 528 MET cc_start: 0.0563 (mmt) cc_final: -0.1165 (mmt) REVERT: e 703 MET cc_start: -0.0822 (ttp) cc_final: -0.1026 (mtm) REVERT: i 19 MET cc_start: -0.3123 (tpp) cc_final: -0.3367 (tpt) REVERT: i 26 MET cc_start: -0.2508 (mmp) cc_final: -0.3949 (tpt) REVERT: j 176 MET cc_start: -0.1453 (mtm) cc_final: -0.3105 (ptt) REVERT: j 197 MET cc_start: -0.3714 (mmt) cc_final: -0.3992 (tpt) REVERT: l 126 MET cc_start: -0.0823 (mtt) cc_final: -0.1699 (mmt) REVERT: o 78 MET cc_start: 0.7128 (tpt) cc_final: 0.6690 (mpp) REVERT: o 217 SER cc_start: 0.8567 (OUTLIER) cc_final: 0.8356 (p) REVERT: o 372 ASN cc_start: 0.8587 (m-40) cc_final: 0.7572 (t0) REVERT: o 393 ILE cc_start: 0.8699 (mt) cc_final: 0.8161 (tp) REVERT: o 459 ASN cc_start: 0.8214 (p0) cc_final: 0.7651 (p0) REVERT: o 463 THR cc_start: 0.6183 (p) cc_final: 0.5560 (p) REVERT: o 470 MET cc_start: 0.7867 (mtm) cc_final: 0.7558 (mtm) REVERT: o 474 VAL cc_start: 0.8812 (t) cc_final: 0.8579 (p) REVERT: o 496 PHE cc_start: 0.8451 (m-80) cc_final: 0.8241 (m-10) REVERT: o 524 MET cc_start: 0.8963 (OUTLIER) cc_final: 0.8603 (mmt) REVERT: o 539 GLN cc_start: 0.6296 (OUTLIER) cc_final: 0.6069 (tm-30) REVERT: o 872 MET cc_start: 0.8206 (ptm) cc_final: 0.7846 (pmm) REVERT: o 1043 ILE cc_start: 0.8994 (mt) cc_final: 0.8723 (mm) REVERT: o 1228 MET cc_start: 0.4566 (ptt) cc_final: 0.3550 (ptt) REVERT: o 1405 MET cc_start: 0.8486 (ttt) cc_final: 0.8097 (tpp) REVERT: o 1440 MET cc_start: 0.7802 (mmt) cc_final: 0.7374 (mmt) REVERT: p 225 LEU cc_start: 0.8248 (pt) cc_final: 0.7866 (tp) REVERT: p 508 MET cc_start: 0.7785 (mtt) cc_final: 0.7195 (mtt) REVERT: p 524 LYS cc_start: 0.8941 (mtmm) cc_final: 0.8480 (mttt) REVERT: p 561 ILE cc_start: 0.7949 (tt) cc_final: 0.7662 (mm) REVERT: p 751 LEU cc_start: 0.8862 (tp) cc_final: 0.8546 (mm) REVERT: p 764 MET cc_start: 0.7927 (mtm) cc_final: 0.7454 (ppp) REVERT: p 779 ILE cc_start: 0.6793 (mt) cc_final: 0.6312 (mm) REVERT: p 789 ASN cc_start: 0.7762 (p0) cc_final: 0.7221 (p0) REVERT: p 840 MET cc_start: 0.5644 (ptp) cc_final: 0.4670 (ptp) REVERT: p 867 ILE cc_start: 0.8323 (mt) cc_final: 0.7798 (mm) REVERT: p 976 MET cc_start: 0.7331 (OUTLIER) cc_final: 0.6790 (mpp) REVERT: p 978 ILE cc_start: 0.7115 (OUTLIER) cc_final: 0.6797 (mt) REVERT: p 1102 PHE cc_start: 0.7189 (t80) cc_final: 0.6960 (t80) REVERT: p 1149 VAL cc_start: 0.7793 (OUTLIER) cc_final: 0.7439 (m) REVERT: p 1151 MET cc_start: 0.6567 (ptm) cc_final: 0.6282 (ttp) REVERT: s 144 LEU cc_start: 0.8860 (mt) cc_final: 0.8297 (mt) REVERT: t 96 GLU cc_start: 0.7608 (mt-10) cc_final: 0.5814 (mm-30) REVERT: v 46 GLN cc_start: 0.8701 (mt0) cc_final: 0.7993 (tp40) REVERT: v 58 LEU cc_start: 0.6956 (tt) cc_final: 0.6686 (tt) REVERT: v 118 TYR cc_start: 0.6458 (m-80) cc_final: 0.5811 (m-80) REVERT: w 49 ASP cc_start: 0.7662 (p0) cc_final: 0.7411 (p0) REVERT: y 11 LEU cc_start: 0.8477 (tp) cc_final: 0.8016 (tt) REVERT: z 18 ILE cc_start: 0.7586 (mt) cc_final: 0.7025 (tp) REVERT: u 59 ILE cc_start: 0.8570 (mt) cc_final: 0.8194 (mt) outliers start: 286 outliers final: 58 residues processed: 1323 average time/residue: 0.7930 time to fit residues: 1761.3352 Evaluate side-chains 646 residues out of total 8741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 574 time to evaluate : 6.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 977 random chunks: chunk 825 optimal weight: 1.9990 chunk 740 optimal weight: 10.0000 chunk 410 optimal weight: 8.9990 chunk 252 optimal weight: 5.9990 chunk 499 optimal weight: 30.0000 chunk 395 optimal weight: 9.9990 chunk 765 optimal weight: 10.0000 chunk 296 optimal weight: 0.9980 chunk 465 optimal weight: 10.0000 chunk 569 optimal weight: 40.0000 chunk 887 optimal weight: 6.9990 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 409 HIS A 741 GLN A 860 ASN ** A1058 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1073 GLN B 30 HIS B 36 ASN B 137 HIS B 183 GLN B 348 GLN B 415 HIS B 439 HIS B 509 ASN ** B 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 576 ASN B 580 GLN B 644 GLN B 652 GLN B 734 ASN B 750 GLN B 813 ASN ** B 866 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 882 HIS B 915 GLN D 956 GLN D1075 HIS E 238 GLN E 254 ASN E 276 GLN E 351 GLN ** E 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 585 ASN E 616 HIS E 636 HIS E 640 ASN E 658 ASN E 673 HIS E 758 HIS F 59 HIS F 119 ASN ** F 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 275 ASN F 316 GLN G 48 HIS G 53 HIS H 145 HIS I 21 GLN I 38 GLN I 98 GLN I 101 GLN I 126 ASN ** J 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 105 HIS L 117 GLN ** O 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 63 ASN P 167 ASN P 242 GLN P 278 GLN ** Q 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 352 HIS Q 361 ASN c 32 HIS d 912 ASN d1069 ASN e 223 HIS e 246 HIS e 294 ASN e 336 HIS e 556 ASN ** f 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 349 ASN i 81 GLN j 173 HIS k 139 GLN ** m 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 123 ASN ** o 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 296 ASN o 313 HIS o 504 HIS ** o 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 620 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 662 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 673 GLN o 678 ASN ** o 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 704 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 723 ASN o 765 ASN ** o 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 809 HIS ** o 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 913 ASN ** o1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o1077 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o1230 GLN o1244 ASN ** o1248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o1332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o1420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o1445 HIS ** o1462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 287 HIS p 410 ASN p 502 HIS p 537 GLN p 593 GLN p 725 GLN p 842 HIS ** p1060 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p1115 GLN q 265 HIS ** r 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 87 GLN v 131 ASN y 29 ASN ** y 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 91 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4031 moved from start: 0.3444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.220 83750 Z= 0.428 Angle : 0.877 18.974 113898 Z= 0.458 Chirality : 0.049 0.325 12709 Planarity : 0.007 0.096 14167 Dihedral : 14.262 162.455 12402 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 17.32 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.60 % Favored : 94.30 % Rotamer: Outliers : 0.39 % Allowed : 5.89 % Favored : 93.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % Cis-general : 0.00 % Twisted Proline : 0.21 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.49 (0.08), residues: 9695 helix: -1.34 (0.08), residues: 3854 sheet: -1.18 (0.14), residues: 1301 loop : -2.01 (0.09), residues: 4540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP A 341 HIS 0.029 0.002 HIS G 134 PHE 0.045 0.003 PHE s 130 TYR 0.035 0.002 TYR p 388 ARG 0.015 0.001 ARG l 106 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19390 Ramachandran restraints generated. 9695 Oldfield, 0 Emsley, 9695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19390 Ramachandran restraints generated. 9695 Oldfield, 0 Emsley, 9695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 679 residues out of total 8741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 645 time to evaluate : 7.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 352 MET cc_start: 0.2445 (ptt) cc_final: 0.0390 (ptt) REVERT: A 662 MET cc_start: -0.2298 (mmp) cc_final: -0.2607 (mmt) REVERT: A 692 MET cc_start: 0.0511 (ttm) cc_final: 0.0114 (ttt) REVERT: F 290 MET cc_start: 0.7875 (tmm) cc_final: 0.7620 (tmm) REVERT: J 121 MET cc_start: -0.1263 (mtt) cc_final: -0.1862 (mtt) REVERT: P 273 LEU cc_start: 0.7280 (tp) cc_final: 0.7012 (tp) REVERT: c 73 MET cc_start: 0.0194 (mmm) cc_final: -0.0478 (mmt) REVERT: e 291 MET cc_start: -0.2684 (tpp) cc_final: -0.3179 (mmt) REVERT: e 442 MET cc_start: 0.2443 (ppp) cc_final: 0.1974 (ppp) REVERT: e 528 MET cc_start: 0.0259 (mmt) cc_final: -0.1496 (mmt) REVERT: i 26 MET cc_start: -0.3136 (mmp) cc_final: -0.3822 (tpt) REVERT: j 197 MET cc_start: -0.3448 (mmt) cc_final: -0.3981 (tpt) REVERT: l 83 MET cc_start: -0.5365 (ttt) cc_final: -0.5976 (ttt) REVERT: l 126 MET cc_start: -0.1106 (mtt) cc_final: -0.1981 (mmt) REVERT: o 85 PHE cc_start: 0.8307 (m-10) cc_final: 0.7462 (m-80) REVERT: o 260 VAL cc_start: 0.9370 (t) cc_final: 0.8812 (t) REVERT: o 388 MET cc_start: 0.8435 (mtt) cc_final: 0.7797 (mmt) REVERT: o 459 ASN cc_start: 0.8796 (p0) cc_final: 0.8117 (p0) REVERT: o 467 MET cc_start: 0.8795 (mmp) cc_final: 0.8028 (mmp) REVERT: o 470 MET cc_start: 0.8745 (mtm) cc_final: 0.8291 (mmm) REVERT: o 484 LEU cc_start: 0.9449 (OUTLIER) cc_final: 0.9191 (pp) REVERT: o 524 MET cc_start: 0.9253 (mtt) cc_final: 0.8618 (mpp) REVERT: o 535 MET cc_start: 0.7001 (mtt) cc_final: 0.6725 (mtt) REVERT: o 637 MET cc_start: 0.8648 (ttp) cc_final: 0.7871 (tmm) REVERT: o 712 ASP cc_start: 0.8446 (t0) cc_final: 0.8070 (t0) REVERT: o 769 MET cc_start: 0.8746 (mtt) cc_final: 0.8520 (mtt) REVERT: o 872 MET cc_start: 0.8299 (ptm) cc_final: 0.7654 (ptt) REVERT: o 950 ASN cc_start: 0.8739 (t0) cc_final: 0.8492 (t0) REVERT: o 1093 GLN cc_start: 0.8432 (pm20) cc_final: 0.8195 (pp30) REVERT: o 1202 PHE cc_start: 0.5300 (t80) cc_final: 0.4957 (t80) REVERT: o 1228 MET cc_start: 0.5388 (ptt) cc_final: 0.5107 (ptt) REVERT: o 1430 CYS cc_start: 0.8473 (p) cc_final: 0.8269 (p) REVERT: o 1440 MET cc_start: 0.7343 (mmt) cc_final: 0.7117 (mmt) REVERT: p 108 MET cc_start: 0.5534 (ptt) cc_final: 0.5304 (ptt) REVERT: p 285 LEU cc_start: 0.8964 (tt) cc_final: 0.8615 (mm) REVERT: p 508 MET cc_start: 0.7528 (mtt) cc_final: 0.7303 (mmt) REVERT: p 672 THR cc_start: 0.8296 (p) cc_final: 0.8028 (t) REVERT: p 694 THR cc_start: 0.8270 (p) cc_final: 0.8031 (t) REVERT: p 728 MET cc_start: 0.8568 (tmm) cc_final: 0.8096 (tmm) REVERT: p 789 ASN cc_start: 0.8113 (p0) cc_final: 0.7400 (p0) REVERT: p 802 ASP cc_start: 0.8883 (m-30) cc_final: 0.8529 (m-30) REVERT: p 933 ASP cc_start: 0.8291 (m-30) cc_final: 0.8060 (m-30) REVERT: p 951 GLN cc_start: 0.7967 (tt0) cc_final: 0.6870 (tm-30) REVERT: p 976 MET cc_start: 0.8861 (mpp) cc_final: 0.8085 (mpp) REVERT: p 1102 PHE cc_start: 0.7737 (t80) cc_final: 0.7313 (t80) REVERT: s 130 PHE cc_start: 0.8462 (m-80) cc_final: 0.8134 (m-80) REVERT: t 61 GLU cc_start: 0.8446 (mt-10) cc_final: 0.7945 (mt-10) REVERT: t 96 GLU cc_start: 0.7898 (mt-10) cc_final: 0.7607 (mt-10) REVERT: v 44 ASN cc_start: 0.8627 (m-40) cc_final: 0.8325 (t0) REVERT: v 112 LEU cc_start: 0.8687 (mt) cc_final: 0.8443 (mt) REVERT: y 11 LEU cc_start: 0.8678 (tp) cc_final: 0.8191 (tt) outliers start: 34 outliers final: 10 residues processed: 677 average time/residue: 0.7577 time to fit residues: 883.2654 Evaluate side-chains 476 residues out of total 8741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 465 time to evaluate : 6.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 977 random chunks: chunk 493 optimal weight: 30.0000 chunk 275 optimal weight: 10.0000 chunk 738 optimal weight: 1.9990 chunk 604 optimal weight: 6.9990 chunk 244 optimal weight: 8.9990 chunk 888 optimal weight: 0.9990 chunk 960 optimal weight: 10.0000 chunk 791 optimal weight: 2.9990 chunk 881 optimal weight: 20.0000 chunk 303 optimal weight: 8.9990 chunk 713 optimal weight: 9.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 802 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1058 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1073 GLN B 59 ASN B 176 HIS B 235 HIS ** B 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 GLN ** B 915 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1005 ASN E 268 HIS E 276 GLN ** E 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 640 ASN F 220 GLN ** F 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 270 ASN F 274 ASN ** I 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 101 GLN J 160 GLN ** O 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 24 GLN P 166 GLN P 256 GLN ** Q 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 104 ASN d 936 GLN e 238 GLN e 320 HIS e 368 ASN f 59 HIS f 220 GLN f 339 GLN f 350 ASN m 107 ASN ** o 677 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 704 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 739 ASN ** o 757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 783 GLN ** o 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 809 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o1005 HIS ** o1077 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o1129 ASN ** o1248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o1332 GLN ** o1420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o1457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 502 HIS ** p 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 749 HIS p 941 GLN p 948 GLN ** p1003 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p1060 HIS ** r 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 64 HIS ** s 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 69 HIS Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4121 moved from start: 0.4344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.170 83750 Z= 0.350 Angle : 0.729 20.018 113898 Z= 0.380 Chirality : 0.045 0.218 12709 Planarity : 0.005 0.080 14167 Dihedral : 14.307 177.245 12402 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 16.93 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.73 % Favored : 94.18 % Rotamer: Outliers : 0.16 % Allowed : 4.48 % Favored : 95.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % Cis-general : 0.00 % Twisted Proline : 0.21 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.08), residues: 9695 helix: -0.59 (0.08), residues: 3898 sheet: -0.87 (0.14), residues: 1299 loop : -1.80 (0.09), residues: 4498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP e 612 HIS 0.011 0.001 HIS p1021 PHE 0.046 0.002 PHE s 130 TYR 0.028 0.002 TYR p 367 ARG 0.016 0.001 ARG p 721 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19390 Ramachandran restraints generated. 9695 Oldfield, 0 Emsley, 9695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19390 Ramachandran restraints generated. 9695 Oldfield, 0 Emsley, 9695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 551 residues out of total 8741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 537 time to evaluate : 7.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 352 MET cc_start: 0.2246 (ptt) cc_final: 0.2045 (ppp) REVERT: A 692 MET cc_start: 0.0467 (ttm) cc_final: -0.0103 (ttt) REVERT: E 355 MET cc_start: 0.1307 (mmm) cc_final: 0.0958 (mmm) REVERT: J 121 MET cc_start: -0.1239 (mtt) cc_final: -0.1777 (mtt) REVERT: R 124 MET cc_start: 0.7509 (ptp) cc_final: 0.7227 (ptm) REVERT: c 73 MET cc_start: 0.0429 (mmm) cc_final: -0.0347 (mmt) REVERT: e 213 MET cc_start: 0.1710 (tpp) cc_final: 0.1510 (tpp) REVERT: e 442 MET cc_start: 0.2170 (ppp) cc_final: 0.1516 (ppp) REVERT: e 528 MET cc_start: 0.0463 (mmt) cc_final: -0.1743 (mmt) REVERT: f 60 MET cc_start: -0.4630 (ttt) cc_final: -0.5885 (ttt) REVERT: i 19 MET cc_start: -0.4794 (tpt) cc_final: -0.5100 (tpt) REVERT: i 26 MET cc_start: -0.3137 (mmp) cc_final: -0.3913 (tpt) REVERT: j 176 MET cc_start: -0.1322 (mtm) cc_final: -0.2786 (ptt) REVERT: j 197 MET cc_start: -0.3185 (mmt) cc_final: -0.3630 (tpt) REVERT: l 126 MET cc_start: -0.0737 (mtt) cc_final: -0.1567 (mmp) REVERT: m 68 MET cc_start: 0.5344 (mmm) cc_final: 0.4598 (mmm) REVERT: o 85 PHE cc_start: 0.8336 (m-10) cc_final: 0.7600 (m-80) REVERT: o 450 MET cc_start: 0.8606 (ttm) cc_final: 0.8382 (ttp) REVERT: o 501 MET cc_start: 0.9256 (mmm) cc_final: 0.8747 (mmt) REVERT: o 524 MET cc_start: 0.9196 (mtt) cc_final: 0.8687 (mpp) REVERT: o 561 MET cc_start: 0.9045 (ttm) cc_final: 0.8760 (ttm) REVERT: o 660 MET cc_start: 0.8378 (mmm) cc_final: 0.8145 (mmm) REVERT: o 676 ILE cc_start: 0.8763 (OUTLIER) cc_final: 0.8421 (tp) REVERT: o 712 ASP cc_start: 0.8264 (t0) cc_final: 0.8005 (t0) REVERT: o 872 MET cc_start: 0.8051 (ptm) cc_final: 0.7409 (ptt) REVERT: o 961 GLU cc_start: 0.8029 (pt0) cc_final: 0.7779 (pt0) REVERT: o 1102 MET cc_start: 0.1611 (ptt) cc_final: 0.0871 (ptt) REVERT: o 1202 PHE cc_start: 0.5384 (t80) cc_final: 0.5035 (t80) REVERT: p 109 MET cc_start: 0.8640 (mpp) cc_final: 0.8235 (mpp) REVERT: p 195 ILE cc_start: 0.8951 (mm) cc_final: 0.8588 (mm) REVERT: p 508 MET cc_start: 0.7691 (mtt) cc_final: 0.7486 (mtt) REVERT: p 594 MET cc_start: 0.6231 (mmp) cc_final: 0.5886 (tmm) REVERT: p 728 MET cc_start: 0.9105 (tmm) cc_final: 0.8837 (tmm) REVERT: p 976 MET cc_start: 0.8583 (mpp) cc_final: 0.7770 (mpp) REVERT: p 1125 MET cc_start: 0.8097 (tpp) cc_final: 0.7760 (ppp) REVERT: s 130 PHE cc_start: 0.8157 (m-80) cc_final: 0.7636 (m-80) REVERT: t 61 GLU cc_start: 0.8518 (mt-10) cc_final: 0.8042 (mt-10) REVERT: t 96 GLU cc_start: 0.8088 (mt-10) cc_final: 0.7871 (mt-10) REVERT: v 112 LEU cc_start: 0.8719 (mt) cc_final: 0.8472 (mt) REVERT: y 11 LEU cc_start: 0.8805 (tp) cc_final: 0.8336 (tt) outliers start: 14 outliers final: 5 residues processed: 550 average time/residue: 0.7751 time to fit residues: 734.0419 Evaluate side-chains 427 residues out of total 8741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 421 time to evaluate : 7.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 977 random chunks: chunk 878 optimal weight: 7.9990 chunk 668 optimal weight: 0.9990 chunk 461 optimal weight: 40.0000 chunk 98 optimal weight: 5.9990 chunk 424 optimal weight: 10.0000 chunk 596 optimal weight: 7.9990 chunk 892 optimal weight: 6.9990 chunk 944 optimal weight: 0.9990 chunk 466 optimal weight: 9.9990 chunk 845 optimal weight: 20.0000 chunk 254 optimal weight: 0.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 802 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1058 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 352 GLN B 462 ASN B 474 ASN ** B 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 915 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 142 GLN ** F 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 101 GLN I 126 ASN L 75 GLN ** O 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 166 GLN ** Q 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 238 GLN o 410 ASN ** o 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 677 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 700 GLN o 704 ASN o 723 ASN o 731 ASN o 757 GLN ** o 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 885 GLN ** o1077 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o1248 ASN ** o1420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o1422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o1457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 287 HIS ** p 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 503 ASN ** p 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 631 GLN p 749 HIS ** p1003 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4123 moved from start: 0.4848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.121 83750 Z= 0.272 Angle : 0.666 17.452 113898 Z= 0.344 Chirality : 0.044 0.222 12709 Planarity : 0.005 0.062 14167 Dihedral : 14.153 176.090 12402 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 15.92 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.54 % Favored : 94.38 % Rotamer: Outliers : 0.03 % Allowed : 3.37 % Favored : 96.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % Cis-general : 0.00 % Twisted Proline : 0.21 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.08), residues: 9695 helix: -0.18 (0.08), residues: 3889 sheet: -0.71 (0.14), residues: 1306 loop : -1.63 (0.09), residues: 4500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP E 612 HIS 0.009 0.001 HIS A 802 PHE 0.023 0.002 PHE q 184 TYR 0.018 0.001 TYR o 657 ARG 0.010 0.000 ARG q 35 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19390 Ramachandran restraints generated. 9695 Oldfield, 0 Emsley, 9695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19390 Ramachandran restraints generated. 9695 Oldfield, 0 Emsley, 9695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 8741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 516 time to evaluate : 7.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 491 MET cc_start: -0.1878 (ptm) cc_final: -0.2437 (ttp) REVERT: E 473 LEU cc_start: 0.4680 (tp) cc_final: 0.4421 (tp) REVERT: J 121 MET cc_start: -0.1147 (mtt) cc_final: -0.1931 (mtt) REVERT: c 73 MET cc_start: 0.0368 (mmm) cc_final: -0.0449 (mmt) REVERT: e 213 MET cc_start: 0.1971 (tpp) cc_final: 0.1668 (tpp) REVERT: e 291 MET cc_start: -0.3766 (mmt) cc_final: -0.4004 (mmt) REVERT: e 442 MET cc_start: 0.2180 (ppp) cc_final: 0.1515 (ppp) REVERT: e 703 MET cc_start: -0.2181 (mtt) cc_final: -0.2571 (mmt) REVERT: e 731 MET cc_start: -0.0833 (mmt) cc_final: -0.1417 (mmt) REVERT: f 26 MET cc_start: -0.4221 (tpt) cc_final: -0.4581 (tpt) REVERT: f 60 MET cc_start: -0.4437 (ttt) cc_final: -0.4731 (ttt) REVERT: f 255 MET cc_start: 0.7715 (ptp) cc_final: 0.6804 (mtm) REVERT: i 26 MET cc_start: -0.3174 (mmp) cc_final: -0.4485 (tpt) REVERT: j 176 MET cc_start: -0.1342 (mtm) cc_final: -0.2796 (ptt) REVERT: j 197 MET cc_start: -0.3234 (mmt) cc_final: -0.3892 (tpt) REVERT: l 126 MET cc_start: -0.0787 (mtt) cc_final: -0.1703 (mmp) REVERT: o 85 PHE cc_start: 0.8343 (m-10) cc_final: 0.7612 (m-80) REVERT: o 450 MET cc_start: 0.8702 (ttm) cc_final: 0.8462 (ttp) REVERT: o 469 MET cc_start: 0.8594 (mtt) cc_final: 0.8330 (mtt) REVERT: o 470 MET cc_start: 0.8355 (mtp) cc_final: 0.8010 (mmm) REVERT: o 501 MET cc_start: 0.9024 (mmm) cc_final: 0.8652 (mmt) REVERT: o 510 GLU cc_start: 0.7738 (tp30) cc_final: 0.7374 (tp30) REVERT: o 524 MET cc_start: 0.9158 (mtt) cc_final: 0.8704 (mpp) REVERT: o 712 ASP cc_start: 0.8434 (t0) cc_final: 0.8068 (t0) REVERT: o 757 GLN cc_start: 0.9045 (OUTLIER) cc_final: 0.8800 (mm-40) REVERT: o 872 MET cc_start: 0.7972 (ptm) cc_final: 0.7269 (ptt) REVERT: o 1102 MET cc_start: 0.1454 (ptt) cc_final: 0.1140 (ptt) REVERT: o 1202 PHE cc_start: 0.5183 (t80) cc_final: 0.4811 (t80) REVERT: o 1228 MET cc_start: 0.5106 (ptt) cc_final: 0.4792 (ptt) REVERT: p 108 MET cc_start: 0.5355 (ptt) cc_final: 0.4779 (ptt) REVERT: p 109 MET cc_start: 0.8634 (mpp) cc_final: 0.8149 (mpp) REVERT: p 486 ASN cc_start: 0.9277 (m110) cc_final: 0.8928 (m-40) REVERT: p 728 MET cc_start: 0.9051 (tmm) cc_final: 0.8619 (tmm) REVERT: p 733 MET cc_start: 0.8631 (ppp) cc_final: 0.8391 (ppp) REVERT: p 976 MET cc_start: 0.8529 (mpp) cc_final: 0.7593 (mpp) REVERT: p 1125 MET cc_start: 0.8211 (tpp) cc_final: 0.7783 (ppp) REVERT: t 61 GLU cc_start: 0.8395 (mt-10) cc_final: 0.7883 (mt-10) REVERT: v 112 LEU cc_start: 0.8852 (mt) cc_final: 0.8450 (mt) REVERT: y 11 LEU cc_start: 0.8881 (tp) cc_final: 0.8593 (tp) outliers start: 3 outliers final: 2 residues processed: 519 average time/residue: 0.7511 time to fit residues: 675.1498 Evaluate side-chains 425 residues out of total 8741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 422 time to evaluate : 6.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 977 random chunks: chunk 786 optimal weight: 0.8980 chunk 536 optimal weight: 40.0000 chunk 13 optimal weight: 0.2980 chunk 703 optimal weight: 5.9990 chunk 389 optimal weight: 50.0000 chunk 805 optimal weight: 0.0870 chunk 652 optimal weight: 6.9990 chunk 1 optimal weight: 0.0770 chunk 482 optimal weight: 40.0000 chunk 847 optimal weight: 20.0000 chunk 238 optimal weight: 9.9990 overall best weight: 1.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 802 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 ASN ** B 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 915 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 220 GLN ** F 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 316 GLN ** G 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 126 ASN L 73 ASN ** L 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 256 GLN ** Q 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 238 GLN i 98 GLN o 620 HIS ** o 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 677 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 700 GLN o 765 ASN ** o 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o1077 ASN ** o1420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o1422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o1457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 287 HIS ** p 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p1003 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p1094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 113 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4074 moved from start: 0.5047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 83750 Z= 0.186 Angle : 0.615 16.226 113898 Z= 0.315 Chirality : 0.043 0.312 12709 Planarity : 0.004 0.095 14167 Dihedral : 14.027 176.808 12402 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.07 % Favored : 94.84 % Rotamer: Outliers : 0.01 % Allowed : 1.99 % Favored : 98.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % Cis-general : 0.00 % Twisted Proline : 0.21 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.08), residues: 9695 helix: 0.11 (0.08), residues: 3886 sheet: -0.48 (0.14), residues: 1281 loop : -1.52 (0.09), residues: 4528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP E 612 HIS 0.013 0.001 HIS L 119 PHE 0.028 0.001 PHE F 259 TYR 0.022 0.001 TYR O 6 ARG 0.037 0.000 ARG o 244 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19390 Ramachandran restraints generated. 9695 Oldfield, 0 Emsley, 9695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19390 Ramachandran restraints generated. 9695 Oldfield, 0 Emsley, 9695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 8741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 505 time to evaluate : 7.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 491 MET cc_start: -0.1625 (ptm) cc_final: -0.2067 (ttm) REVERT: J 121 MET cc_start: -0.1292 (mtt) cc_final: -0.2290 (mtt) REVERT: R 124 MET cc_start: 0.7393 (ptp) cc_final: 0.7190 (ptt) REVERT: c 73 MET cc_start: 0.0200 (mmm) cc_final: -0.0616 (mmt) REVERT: e 442 MET cc_start: 0.2299 (ppp) cc_final: 0.1516 (ppp) REVERT: e 528 MET cc_start: -0.0041 (mmt) cc_final: -0.1869 (mmt) REVERT: e 703 MET cc_start: -0.1536 (mtt) cc_final: -0.2082 (mmt) REVERT: f 26 MET cc_start: -0.4286 (tpt) cc_final: -0.4716 (tpt) REVERT: f 255 MET cc_start: 0.7663 (ptp) cc_final: 0.6727 (mtm) REVERT: i 26 MET cc_start: -0.3163 (mmp) cc_final: -0.3967 (tpt) REVERT: j 176 MET cc_start: -0.1353 (mtm) cc_final: -0.2799 (ptt) REVERT: j 197 MET cc_start: -0.3221 (mmt) cc_final: -0.3896 (tpt) REVERT: l 126 MET cc_start: -0.0702 (mtt) cc_final: -0.1682 (mmp) REVERT: m 68 MET cc_start: 0.5586 (mmm) cc_final: 0.4940 (mmm) REVERT: o 85 PHE cc_start: 0.8314 (m-10) cc_final: 0.7607 (m-80) REVERT: o 388 MET cc_start: 0.8731 (mtt) cc_final: 0.8525 (mtt) REVERT: o 450 MET cc_start: 0.8693 (ttm) cc_final: 0.8479 (ttp) REVERT: o 467 MET cc_start: 0.8967 (mmp) cc_final: 0.8703 (mmm) REVERT: o 501 MET cc_start: 0.8986 (mmm) cc_final: 0.8597 (mmt) REVERT: o 524 MET cc_start: 0.9093 (mtt) cc_final: 0.8800 (mpp) REVERT: o 637 MET cc_start: 0.8830 (ppp) cc_final: 0.8510 (ppp) REVERT: o 712 ASP cc_start: 0.8372 (t0) cc_final: 0.8018 (t0) REVERT: o 872 MET cc_start: 0.7989 (ptm) cc_final: 0.7295 (ptt) REVERT: o 1102 MET cc_start: 0.1768 (ptt) cc_final: 0.1338 (ptt) REVERT: o 1202 PHE cc_start: 0.5247 (t80) cc_final: 0.4830 (t80) REVERT: o 1228 MET cc_start: 0.5231 (ptt) cc_final: 0.4977 (ptt) REVERT: o 1262 MET cc_start: 0.8103 (ptp) cc_final: 0.7786 (ptt) REVERT: p 108 MET cc_start: 0.5303 (ptt) cc_final: 0.4652 (ptt) REVERT: p 109 MET cc_start: 0.8571 (mpp) cc_final: 0.8168 (mpp) REVERT: p 529 MET cc_start: 0.8594 (mmt) cc_final: 0.8378 (mmm) REVERT: p 702 MET cc_start: 0.9373 (mmm) cc_final: 0.9136 (mmp) REVERT: p 728 MET cc_start: 0.8994 (tmm) cc_final: 0.8776 (tmm) REVERT: p 1163 MET cc_start: 0.7552 (mmt) cc_final: 0.7328 (mmt) REVERT: q 61 ASP cc_start: 0.8673 (m-30) cc_final: 0.8467 (m-30) REVERT: s 94 MET cc_start: 0.8572 (ttt) cc_final: 0.8300 (ttt) REVERT: t 61 GLU cc_start: 0.8265 (mt-10) cc_final: 0.7265 (mp0) REVERT: v 112 LEU cc_start: 0.8711 (mt) cc_final: 0.8337 (mt) REVERT: y 11 LEU cc_start: 0.8860 (tp) cc_final: 0.8593 (tp) outliers start: 1 outliers final: 0 residues processed: 506 average time/residue: 0.7518 time to fit residues: 663.7233 Evaluate side-chains 410 residues out of total 8741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 410 time to evaluate : 7.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 977 random chunks: chunk 317 optimal weight: 50.0000 chunk 850 optimal weight: 0.9990 chunk 186 optimal weight: 0.7980 chunk 554 optimal weight: 20.0000 chunk 233 optimal weight: 0.0370 chunk 945 optimal weight: 0.1980 chunk 784 optimal weight: 0.1980 chunk 437 optimal weight: 9.9990 chunk 78 optimal weight: 5.9990 chunk 312 optimal weight: 4.9990 chunk 496 optimal weight: 0.3980 overall best weight: 0.3258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 802 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 HIS B 331 HIS B 474 ASN ** B 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 734 ASN ** B 915 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 142 GLN ** F 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 126 ASN ** O 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 63 ASN P 166 GLN P 256 GLN ** Q 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 238 GLN ** o 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 677 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 721 HIS ** o1077 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o1422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o1457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 970 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p1003 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p1094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 135 GLN ** w 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4009 moved from start: 0.5192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 83750 Z= 0.149 Angle : 0.589 16.768 113898 Z= 0.301 Chirality : 0.042 0.227 12709 Planarity : 0.004 0.054 14167 Dihedral : 13.817 177.392 12402 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.66 % Favored : 95.26 % Rotamer: Outliers : 0.02 % Allowed : 1.84 % Favored : 98.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % Cis-general : 0.00 % Twisted Proline : 0.21 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.09), residues: 9695 helix: 0.37 (0.09), residues: 3878 sheet: -0.35 (0.14), residues: 1297 loop : -1.38 (0.09), residues: 4520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP E 612 HIS 0.012 0.001 HIS o 721 PHE 0.022 0.001 PHE d1083 TYR 0.018 0.001 TYR v 97 ARG 0.011 0.000 ARG v 140 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19390 Ramachandran restraints generated. 9695 Oldfield, 0 Emsley, 9695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19390 Ramachandran restraints generated. 9695 Oldfield, 0 Emsley, 9695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 8741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 530 time to evaluate : 6.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 491 MET cc_start: -0.1880 (ptm) cc_final: -0.2202 (ttm) REVERT: B 607 MET cc_start: 0.0565 (ppp) cc_final: -0.0157 (pmm) REVERT: B 612 VAL cc_start: -0.0574 (p) cc_final: -0.0888 (p) REVERT: E 439 ASP cc_start: 0.5483 (t0) cc_final: 0.5204 (t0) REVERT: E 443 ASN cc_start: 0.5656 (m110) cc_final: 0.5440 (m110) REVERT: J 121 MET cc_start: -0.1488 (mtt) cc_final: -0.2240 (mtt) REVERT: c 73 MET cc_start: 0.0193 (mmm) cc_final: -0.0641 (mmt) REVERT: e 213 MET cc_start: 0.1164 (tpp) cc_final: 0.0831 (tpp) REVERT: e 442 MET cc_start: 0.2270 (ppp) cc_final: 0.1522 (ppp) REVERT: e 528 MET cc_start: -0.0149 (mmt) cc_final: -0.2061 (mmt) REVERT: e 703 MET cc_start: -0.1725 (mtt) cc_final: -0.2057 (mmt) REVERT: e 731 MET cc_start: -0.0252 (mmt) cc_final: -0.0893 (mmp) REVERT: f 26 MET cc_start: -0.4248 (tpt) cc_final: -0.4646 (tpt) REVERT: f 255 MET cc_start: 0.7611 (ptp) cc_final: 0.6668 (mtm) REVERT: i 26 MET cc_start: -0.3192 (mmp) cc_final: -0.3945 (tpt) REVERT: j 176 MET cc_start: -0.1407 (mtm) cc_final: -0.2931 (ptt) REVERT: j 197 MET cc_start: -0.3239 (mmt) cc_final: -0.3840 (tpt) REVERT: k 154 MET cc_start: -0.3711 (tpt) cc_final: -0.3957 (tpp) REVERT: l 126 MET cc_start: -0.0975 (mtt) cc_final: -0.1687 (mmp) REVERT: l 152 MET cc_start: -0.2317 (tpp) cc_final: -0.3207 (mpp) REVERT: o 85 PHE cc_start: 0.8275 (m-10) cc_final: 0.7510 (m-80) REVERT: o 388 MET cc_start: 0.8534 (mtt) cc_final: 0.8252 (mtt) REVERT: o 467 MET cc_start: 0.8965 (mmp) cc_final: 0.8708 (mmm) REVERT: o 501 MET cc_start: 0.8820 (mmm) cc_final: 0.8573 (mmt) REVERT: o 510 GLU cc_start: 0.7340 (tp30) cc_final: 0.7018 (tp30) REVERT: o 637 MET cc_start: 0.8784 (ppp) cc_final: 0.8478 (ppp) REVERT: o 712 ASP cc_start: 0.8270 (t0) cc_final: 0.7946 (t0) REVERT: o 872 MET cc_start: 0.7810 (ptm) cc_final: 0.7454 (ptp) REVERT: o 1102 MET cc_start: 0.2011 (ptt) cc_final: 0.1788 (ptt) REVERT: o 1202 PHE cc_start: 0.5115 (t80) cc_final: 0.4734 (t80) REVERT: o 1228 MET cc_start: 0.5514 (ptt) cc_final: 0.5234 (ptt) REVERT: o 1262 MET cc_start: 0.8001 (ptp) cc_final: 0.7606 (ptt) REVERT: p 108 MET cc_start: 0.5269 (ptt) cc_final: 0.4667 (ptt) REVERT: p 109 MET cc_start: 0.8483 (mpp) cc_final: 0.8017 (mpp) REVERT: p 702 MET cc_start: 0.9303 (mmm) cc_final: 0.8980 (mmp) REVERT: p 728 MET cc_start: 0.8936 (tmm) cc_final: 0.8501 (tmm) REVERT: p 976 MET cc_start: 0.8755 (mmm) cc_final: 0.8202 (mmt) REVERT: p 1125 MET cc_start: 0.8467 (ppp) cc_final: 0.7677 (mmt) REVERT: p 1151 MET cc_start: 0.8667 (ppp) cc_final: 0.7927 (tmm) REVERT: p 1163 MET cc_start: 0.7535 (mmt) cc_final: 0.7292 (mmt) REVERT: s 151 MET cc_start: 0.7214 (ptp) cc_final: 0.6240 (ptp) REVERT: t 61 GLU cc_start: 0.8194 (mt-10) cc_final: 0.7261 (mp0) REVERT: v 112 LEU cc_start: 0.8656 (mt) cc_final: 0.8283 (mt) outliers start: 2 outliers final: 1 residues processed: 532 average time/residue: 0.7353 time to fit residues: 682.8062 Evaluate side-chains 419 residues out of total 8741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 418 time to evaluate : 7.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 977 random chunks: chunk 911 optimal weight: 0.0980 chunk 106 optimal weight: 40.0000 chunk 538 optimal weight: 5.9990 chunk 690 optimal weight: 4.9990 chunk 534 optimal weight: 0.0270 chunk 795 optimal weight: 10.0000 chunk 527 optimal weight: 0.4980 chunk 941 optimal weight: 4.9990 chunk 589 optimal weight: 40.0000 chunk 574 optimal weight: 20.0000 chunk 434 optimal weight: 2.9990 overall best weight: 1.7242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 802 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 ASN B 521 GLN ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 915 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 275 ASN ** I 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 126 ASN ** L 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 256 GLN ** S 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 91 GLN e 238 GLN ** o 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 677 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 678 ASN o 721 HIS ** o 809 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o1077 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o1422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o1457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 503 ASN ** p 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p1003 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p1094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p1129 ASN r 129 GLN v 126 GLN ** w 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 21 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4072 moved from start: 0.5453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 83750 Z= 0.188 Angle : 0.604 16.485 113898 Z= 0.308 Chirality : 0.042 0.292 12709 Planarity : 0.004 0.052 14167 Dihedral : 13.757 179.290 12402 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.98 % Favored : 94.94 % Rotamer: Outliers : 0.01 % Allowed : 1.18 % Favored : 98.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % Cis-general : 0.00 % Twisted Proline : 0.21 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.09), residues: 9695 helix: 0.59 (0.09), residues: 3870 sheet: -0.34 (0.14), residues: 1299 loop : -1.29 (0.09), residues: 4526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP E 612 HIS 0.016 0.001 HIS B 393 PHE 0.019 0.001 PHE p 50 TYR 0.018 0.001 TYR v 115 ARG 0.010 0.000 ARG p1091 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19390 Ramachandran restraints generated. 9695 Oldfield, 0 Emsley, 9695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19390 Ramachandran restraints generated. 9695 Oldfield, 0 Emsley, 9695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 8741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 511 time to evaluate : 7.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 612 VAL cc_start: -0.0349 (p) cc_final: -0.0720 (p) REVERT: E 439 ASP cc_start: 0.5504 (t0) cc_final: 0.5193 (t0) REVERT: J 121 MET cc_start: -0.1394 (mtt) cc_final: -0.2304 (mtt) REVERT: c 73 MET cc_start: 0.0051 (mmm) cc_final: -0.0788 (mmt) REVERT: e 213 MET cc_start: 0.0710 (tpp) cc_final: 0.0509 (tpp) REVERT: e 442 MET cc_start: 0.2362 (ppp) cc_final: 0.1671 (ppp) REVERT: e 528 MET cc_start: 0.0105 (mmt) cc_final: -0.1905 (mmt) REVERT: e 703 MET cc_start: -0.1648 (mtt) cc_final: -0.2442 (mmt) REVERT: e 731 MET cc_start: -0.0409 (mmt) cc_final: -0.0990 (mmp) REVERT: f 26 MET cc_start: -0.4103 (tpt) cc_final: -0.5973 (tpt) REVERT: f 255 MET cc_start: 0.7546 (ptp) cc_final: 0.6710 (mtm) REVERT: i 26 MET cc_start: -0.3267 (mmp) cc_final: -0.4089 (tpt) REVERT: j 176 MET cc_start: -0.1398 (mtm) cc_final: -0.2890 (ptt) REVERT: j 197 MET cc_start: -0.3210 (mmt) cc_final: -0.3832 (tpt) REVERT: k 154 MET cc_start: -0.3430 (tpt) cc_final: -0.3746 (tpp) REVERT: l 126 MET cc_start: -0.0690 (mtt) cc_final: -0.1529 (mmp) REVERT: l 152 MET cc_start: -0.2340 (tpp) cc_final: -0.2993 (mpp) REVERT: m 68 MET cc_start: 0.5302 (mmm) cc_final: 0.4623 (mmm) REVERT: o 85 PHE cc_start: 0.8300 (m-10) cc_final: 0.7554 (m-80) REVERT: o 388 MET cc_start: 0.8646 (mtt) cc_final: 0.8332 (mtt) REVERT: o 469 MET cc_start: 0.8786 (mmt) cc_final: 0.8417 (mmt) REVERT: o 501 MET cc_start: 0.8723 (mmm) cc_final: 0.8457 (mmt) REVERT: o 510 GLU cc_start: 0.7531 (tp30) cc_final: 0.7141 (tp30) REVERT: o 524 MET cc_start: 0.9270 (mpp) cc_final: 0.8873 (mpp) REVERT: o 637 MET cc_start: 0.9089 (ppp) cc_final: 0.8847 (ppp) REVERT: o 872 MET cc_start: 0.8001 (ptm) cc_final: 0.7252 (ptt) REVERT: o 1161 LEU cc_start: 0.9474 (mt) cc_final: 0.9250 (pp) REVERT: o 1228 MET cc_start: 0.5330 (ptt) cc_final: 0.4975 (ptt) REVERT: o 1235 ILE cc_start: 0.9449 (tp) cc_final: 0.9137 (pt) REVERT: o 1262 MET cc_start: 0.7999 (ptp) cc_final: 0.7550 (ptt) REVERT: o 1336 LEU cc_start: 0.8999 (mm) cc_final: 0.8768 (mm) REVERT: p 108 MET cc_start: 0.5485 (ptt) cc_final: 0.4872 (ptt) REVERT: p 109 MET cc_start: 0.8565 (mpp) cc_final: 0.8105 (mpp) REVERT: p 674 MET cc_start: 0.8163 (ttp) cc_final: 0.7715 (ttp) REVERT: p 728 MET cc_start: 0.8962 (tmm) cc_final: 0.8569 (tmm) REVERT: p 921 ILE cc_start: 0.8635 (mm) cc_final: 0.8428 (mm) REVERT: p 1125 MET cc_start: 0.8472 (ppp) cc_final: 0.7711 (mmt) REVERT: p 1151 MET cc_start: 0.8767 (ppp) cc_final: 0.8034 (tmm) REVERT: p 1163 MET cc_start: 0.7554 (mmt) cc_final: 0.7291 (mmt) REVERT: s 151 MET cc_start: 0.7230 (ptp) cc_final: 0.6246 (ptp) REVERT: t 61 GLU cc_start: 0.8214 (mt-10) cc_final: 0.7387 (mp0) REVERT: v 112 LEU cc_start: 0.8717 (mt) cc_final: 0.8308 (mt) outliers start: 1 outliers final: 0 residues processed: 512 average time/residue: 0.7488 time to fit residues: 667.9132 Evaluate side-chains 410 residues out of total 8741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 410 time to evaluate : 6.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 977 random chunks: chunk 582 optimal weight: 0.4980 chunk 376 optimal weight: 0.0040 chunk 562 optimal weight: 2.9990 chunk 283 optimal weight: 7.9990 chunk 185 optimal weight: 20.0000 chunk 182 optimal weight: 20.0000 chunk 598 optimal weight: 10.0000 chunk 641 optimal weight: 0.7980 chunk 465 optimal weight: 30.0000 chunk 87 optimal weight: 10.0000 chunk 740 optimal weight: 2.9990 overall best weight: 1.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 802 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 ASN ** B 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 915 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 214 HIS ** F 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 326 HIS ** I 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 126 ASN ** L 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 256 GLN ** S 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 238 GLN ** o 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 677 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 721 HIS ** o 809 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o1077 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o1410 HIS ** o1422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o1457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 970 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p1094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 69 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4067 moved from start: 0.5644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 83750 Z= 0.171 Angle : 0.587 16.874 113898 Z= 0.299 Chirality : 0.042 0.314 12709 Planarity : 0.004 0.055 14167 Dihedral : 13.703 179.895 12402 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.93 % Favored : 94.99 % Rotamer: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % Cis-general : 0.00 % Twisted Proline : 0.21 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.09), residues: 9695 helix: 0.70 (0.09), residues: 3861 sheet: -0.24 (0.14), residues: 1328 loop : -1.24 (0.09), residues: 4506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 612 HIS 0.009 0.001 HIS p 970 PHE 0.025 0.001 PHE F 259 TYR 0.022 0.001 TYR z 41 ARG 0.015 0.000 ARG A 798 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19390 Ramachandran restraints generated. 9695 Oldfield, 0 Emsley, 9695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19390 Ramachandran restraints generated. 9695 Oldfield, 0 Emsley, 9695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 8741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 494 time to evaluate : 7.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 212 MET cc_start: 0.0813 (tpt) cc_final: 0.0347 (tpt) REVERT: B 607 MET cc_start: 0.0524 (ppp) cc_final: -0.0126 (pmm) REVERT: B 612 VAL cc_start: 0.0008 (p) cc_final: -0.0317 (p) REVERT: E 355 MET cc_start: 0.0980 (mmm) cc_final: 0.0479 (mmm) REVERT: E 439 ASP cc_start: 0.5595 (t0) cc_final: 0.5275 (t0) REVERT: E 443 ASN cc_start: 0.6084 (m110) cc_final: 0.5861 (m110) REVERT: J 121 MET cc_start: -0.1374 (mtt) cc_final: -0.2285 (mtt) REVERT: c 73 MET cc_start: -0.0221 (mmm) cc_final: -0.1038 (mmt) REVERT: e 213 MET cc_start: 0.0969 (tpp) cc_final: 0.0684 (tpp) REVERT: e 442 MET cc_start: 0.2365 (ppp) cc_final: 0.1687 (ppp) REVERT: e 528 MET cc_start: -0.0153 (mmt) cc_final: -0.2179 (mmt) REVERT: e 703 MET cc_start: -0.1563 (mtt) cc_final: -0.2437 (mmt) REVERT: e 731 MET cc_start: -0.0395 (mmt) cc_final: -0.0938 (mmp) REVERT: f 26 MET cc_start: -0.3986 (tpt) cc_final: -0.5570 (tpt) REVERT: f 255 MET cc_start: 0.7535 (ptp) cc_final: 0.6687 (mtm) REVERT: i 26 MET cc_start: -0.3269 (mmp) cc_final: -0.4093 (tpt) REVERT: j 176 MET cc_start: -0.1403 (mtm) cc_final: -0.2993 (ptt) REVERT: j 197 MET cc_start: -0.3301 (mmt) cc_final: -0.3796 (tpt) REVERT: k 154 MET cc_start: -0.3483 (tpt) cc_final: -0.3778 (tpp) REVERT: l 83 MET cc_start: -0.5404 (ttt) cc_final: -0.5621 (ttt) REVERT: l 126 MET cc_start: -0.0935 (mtt) cc_final: -0.1695 (mmp) REVERT: l 152 MET cc_start: -0.2149 (tpp) cc_final: -0.2680 (mpp) REVERT: o 85 PHE cc_start: 0.8327 (m-10) cc_final: 0.7631 (m-80) REVERT: o 388 MET cc_start: 0.8643 (mtt) cc_final: 0.8300 (mtt) REVERT: o 470 MET cc_start: 0.7757 (mtp) cc_final: 0.7289 (mmm) REVERT: o 501 MET cc_start: 0.8535 (mmm) cc_final: 0.8164 (mmt) REVERT: o 510 GLU cc_start: 0.7503 (tp30) cc_final: 0.7167 (tp30) REVERT: o 524 MET cc_start: 0.9290 (mpp) cc_final: 0.8854 (mpp) REVERT: o 637 MET cc_start: 0.9085 (ppp) cc_final: 0.8838 (ppp) REVERT: o 872 MET cc_start: 0.7938 (ptm) cc_final: 0.7529 (ptp) REVERT: o 1161 LEU cc_start: 0.9528 (mt) cc_final: 0.9295 (pp) REVERT: o 1228 MET cc_start: 0.5768 (ptt) cc_final: 0.5307 (ptt) REVERT: o 1262 MET cc_start: 0.7971 (ptp) cc_final: 0.7698 (ptt) REVERT: p 108 MET cc_start: 0.5217 (ptt) cc_final: 0.4958 (ptt) REVERT: p 109 MET cc_start: 0.8503 (mpp) cc_final: 0.8024 (mpp) REVERT: p 674 MET cc_start: 0.8213 (ttp) cc_final: 0.7895 (ttp) REVERT: p 728 MET cc_start: 0.8966 (tmm) cc_final: 0.8585 (tmm) REVERT: p 952 GLU cc_start: 0.9156 (pm20) cc_final: 0.8919 (pm20) REVERT: p 1125 MET cc_start: 0.8462 (ppp) cc_final: 0.7763 (tpt) REVERT: s 151 MET cc_start: 0.7131 (ptp) cc_final: 0.6180 (ptp) REVERT: t 61 GLU cc_start: 0.8258 (mt-10) cc_final: 0.7405 (mp0) REVERT: v 112 LEU cc_start: 0.8680 (mt) cc_final: 0.8267 (mt) REVERT: y 113 GLN cc_start: 0.6851 (mm110) cc_final: 0.6416 (pm20) outliers start: 0 outliers final: 0 residues processed: 494 average time/residue: 0.8044 time to fit residues: 700.4613 Evaluate side-chains 409 residues out of total 8741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 409 time to evaluate : 7.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 977 random chunks: chunk 856 optimal weight: 0.7980 chunk 902 optimal weight: 8.9990 chunk 823 optimal weight: 2.9990 chunk 877 optimal weight: 6.9990 chunk 901 optimal weight: 3.9990 chunk 528 optimal weight: 9.9990 chunk 382 optimal weight: 8.9990 chunk 689 optimal weight: 0.9990 chunk 269 optimal weight: 9.9990 chunk 792 optimal weight: 1.9990 chunk 829 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 687 ASN ** A 802 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 ASN ** B 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 915 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 15 GLN ** I 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 315 GLN ** S 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 238 GLN ** e 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 62 GLN ** o 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 677 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 721 HIS ** o 809 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o1077 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o1422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o1457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 930 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 970 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 992 ASN ** p1094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4090 moved from start: 0.5841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 83750 Z= 0.184 Angle : 0.590 16.763 113898 Z= 0.301 Chirality : 0.042 0.254 12709 Planarity : 0.004 0.070 14167 Dihedral : 13.684 179.378 12402 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.00 % Favored : 94.90 % Rotamer: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % Cis-general : 0.00 % Twisted Proline : 0.21 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.09), residues: 9695 helix: 0.79 (0.09), residues: 3856 sheet: -0.19 (0.14), residues: 1316 loop : -1.20 (0.09), residues: 4523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP E 612 HIS 0.008 0.001 HIS p 970 PHE 0.051 0.001 PHE o 234 TYR 0.023 0.001 TYR p1048 ARG 0.007 0.000 ARG B 657 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19390 Ramachandran restraints generated. 9695 Oldfield, 0 Emsley, 9695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19390 Ramachandran restraints generated. 9695 Oldfield, 0 Emsley, 9695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 8741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 493 time to evaluate : 7.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 662 MET cc_start: -0.2226 (mmp) cc_final: -0.2431 (mmt) REVERT: A 757 MET cc_start: -0.3107 (tpt) cc_final: -0.3497 (tmm) REVERT: B 212 MET cc_start: 0.0830 (tpt) cc_final: 0.0331 (tpt) REVERT: B 607 MET cc_start: 0.0275 (ppp) cc_final: -0.0553 (pmm) REVERT: B 612 VAL cc_start: 0.0461 (p) cc_final: 0.0135 (p) REVERT: E 355 MET cc_start: 0.1167 (mmm) cc_final: 0.0568 (mmm) REVERT: E 439 ASP cc_start: 0.5635 (t0) cc_final: 0.5343 (t0) REVERT: E 443 ASN cc_start: 0.6143 (m110) cc_final: 0.5344 (m110) REVERT: I 19 MET cc_start: -0.2124 (tmm) cc_final: -0.2364 (tpt) REVERT: J 121 MET cc_start: -0.1305 (mtt) cc_final: -0.2281 (mtt) REVERT: c 73 MET cc_start: -0.0141 (mmm) cc_final: -0.0893 (mmt) REVERT: e 213 MET cc_start: 0.1133 (tpp) cc_final: 0.0883 (tpp) REVERT: e 442 MET cc_start: 0.2558 (ppp) cc_final: 0.1872 (ppp) REVERT: e 528 MET cc_start: -0.0203 (mmt) cc_final: -0.2146 (mmt) REVERT: e 703 MET cc_start: -0.1431 (mtt) cc_final: -0.2257 (mmt) REVERT: e 731 MET cc_start: -0.0221 (mmt) cc_final: -0.0720 (mmp) REVERT: f 26 MET cc_start: -0.3967 (tpt) cc_final: -0.5516 (tpt) REVERT: f 255 MET cc_start: 0.7556 (ptp) cc_final: 0.6712 (mtt) REVERT: i 26 MET cc_start: -0.3204 (mmp) cc_final: -0.4091 (tpt) REVERT: j 197 MET cc_start: -0.3186 (mmt) cc_final: -0.3777 (tpt) REVERT: l 126 MET cc_start: -0.0941 (mtt) cc_final: -0.1733 (mmp) REVERT: l 152 MET cc_start: -0.2097 (tpp) cc_final: -0.2732 (mpp) REVERT: m 68 MET cc_start: 0.5420 (mmm) cc_final: 0.4707 (mmm) REVERT: o 85 PHE cc_start: 0.8348 (m-10) cc_final: 0.7629 (m-80) REVERT: o 388 MET cc_start: 0.8647 (mtt) cc_final: 0.8311 (mtt) REVERT: o 501 MET cc_start: 0.8578 (mmm) cc_final: 0.8295 (mmt) REVERT: o 561 MET cc_start: 0.8722 (ttm) cc_final: 0.8199 (tpp) REVERT: o 637 MET cc_start: 0.9157 (ppp) cc_final: 0.8907 (ppp) REVERT: o 872 MET cc_start: 0.8029 (ptm) cc_final: 0.7251 (ptt) REVERT: o 1202 PHE cc_start: 0.5352 (t80) cc_final: 0.5015 (t80) REVERT: o 1228 MET cc_start: 0.5724 (ptt) cc_final: 0.5215 (ptt) REVERT: o 1336 LEU cc_start: 0.8947 (mm) cc_final: 0.8691 (mm) REVERT: p 108 MET cc_start: 0.5295 (ptt) cc_final: 0.5060 (ptt) REVERT: p 109 MET cc_start: 0.8519 (mpp) cc_final: 0.8056 (mpp) REVERT: p 368 MET cc_start: 0.7809 (ttt) cc_final: 0.7455 (ppp) REVERT: p 674 MET cc_start: 0.8472 (ttp) cc_final: 0.8233 (ttp) REVERT: p 728 MET cc_start: 0.8911 (tmm) cc_final: 0.8594 (tmm) REVERT: p 952 GLU cc_start: 0.9140 (pm20) cc_final: 0.8890 (pm20) REVERT: p 1090 GLU cc_start: 0.8894 (mm-30) cc_final: 0.8530 (mm-30) REVERT: p 1125 MET cc_start: 0.8453 (ppp) cc_final: 0.7743 (mmt) REVERT: p 1163 MET cc_start: 0.7570 (mmt) cc_final: 0.7260 (mmt) REVERT: s 151 MET cc_start: 0.7258 (ptp) cc_final: 0.6316 (ptp) REVERT: t 61 GLU cc_start: 0.8219 (mt-10) cc_final: 0.7463 (mp0) REVERT: v 112 LEU cc_start: 0.8787 (mt) cc_final: 0.8339 (mt) REVERT: y 113 GLN cc_start: 0.6853 (mm110) cc_final: 0.6398 (pm20) outliers start: 0 outliers final: 0 residues processed: 493 average time/residue: 0.7803 time to fit residues: 694.5223 Evaluate side-chains 406 residues out of total 8741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 406 time to evaluate : 7.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 977 random chunks: chunk 874 optimal weight: 0.3980 chunk 576 optimal weight: 10.0000 chunk 927 optimal weight: 0.4980 chunk 566 optimal weight: 0.4980 chunk 440 optimal weight: 10.0000 chunk 645 optimal weight: 0.5980 chunk 973 optimal weight: 0.0980 chunk 895 optimal weight: 8.9990 chunk 775 optimal weight: 6.9990 chunk 80 optimal weight: 0.9990 chunk 598 optimal weight: 3.9990 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 802 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 ASN ** B 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 915 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 15 GLN ** I 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 60 HIS ** I 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 173 HIS ** L 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 238 GLN e 631 ASN ** e 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 721 HIS ** o 809 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 997 ASN ** o1077 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o1422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o1457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 970 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p1094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4029 moved from start: 0.5918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 83750 Z= 0.144 Angle : 0.577 17.093 113898 Z= 0.292 Chirality : 0.042 0.241 12709 Planarity : 0.004 0.051 14167 Dihedral : 13.586 179.230 12402 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.52 % Favored : 95.40 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % Cis-general : 0.00 % Twisted Proline : 0.21 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.09), residues: 9695 helix: 0.88 (0.09), residues: 3845 sheet: -0.10 (0.14), residues: 1290 loop : -1.14 (0.09), residues: 4560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP q 176 HIS 0.014 0.001 HIS p 749 PHE 0.020 0.001 PHE H 193 TYR 0.020 0.001 TYR z 41 ARG 0.008 0.000 ARG o 61 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19390 Ramachandran restraints generated. 9695 Oldfield, 0 Emsley, 9695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19390 Ramachandran restraints generated. 9695 Oldfield, 0 Emsley, 9695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 8741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 501 time to evaluate : 7.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 757 MET cc_start: -0.3186 (tpt) cc_final: -0.3548 (tmm) REVERT: B 212 MET cc_start: 0.0804 (tpt) cc_final: 0.0384 (tpt) REVERT: B 612 VAL cc_start: 0.0254 (p) cc_final: -0.0160 (p) REVERT: B 719 MET cc_start: 0.5099 (mmp) cc_final: 0.4520 (mmp) REVERT: E 355 MET cc_start: 0.0889 (mmm) cc_final: 0.0457 (mmm) REVERT: E 439 ASP cc_start: 0.5848 (t0) cc_final: 0.5586 (t0) REVERT: E 443 ASN cc_start: 0.6045 (m110) cc_final: 0.5245 (m110) REVERT: E 473 LEU cc_start: 0.4627 (tp) cc_final: 0.4426 (tp) REVERT: J 121 MET cc_start: -0.1389 (mtt) cc_final: -0.2327 (mtt) REVERT: R 124 MET cc_start: 0.7188 (ptp) cc_final: 0.6893 (ptt) REVERT: c 73 MET cc_start: -0.0072 (mmm) cc_final: -0.0846 (mmt) REVERT: e 213 MET cc_start: 0.1144 (tpp) cc_final: 0.0870 (tpp) REVERT: e 442 MET cc_start: 0.2576 (ppp) cc_final: 0.1866 (ppp) REVERT: e 528 MET cc_start: -0.0047 (mmt) cc_final: -0.2063 (mmt) REVERT: e 703 MET cc_start: -0.0804 (mtt) cc_final: -0.1836 (mmt) REVERT: e 731 MET cc_start: -0.0253 (mmt) cc_final: -0.0756 (mmp) REVERT: f 26 MET cc_start: -0.3982 (tpt) cc_final: -0.5512 (tpt) REVERT: f 255 MET cc_start: 0.7454 (ptp) cc_final: 0.6675 (mtt) REVERT: i 26 MET cc_start: -0.3208 (mmp) cc_final: -0.4065 (tpt) REVERT: j 197 MET cc_start: -0.3234 (mmt) cc_final: -0.3735 (tpt) REVERT: l 83 MET cc_start: -0.5375 (ttt) cc_final: -0.5612 (ttt) REVERT: l 126 MET cc_start: -0.1177 (mtt) cc_final: -0.1913 (mmp) REVERT: l 152 MET cc_start: -0.2134 (tpp) cc_final: -0.2801 (mpp) REVERT: m 68 MET cc_start: 0.5428 (mmm) cc_final: 0.4884 (mmm) REVERT: o 85 PHE cc_start: 0.8337 (m-10) cc_final: 0.7641 (m-80) REVERT: o 388 MET cc_start: 0.8553 (mtt) cc_final: 0.8099 (mtt) REVERT: o 450 MET cc_start: 0.8453 (ttp) cc_final: 0.8250 (ttp) REVERT: o 501 MET cc_start: 0.8500 (mmm) cc_final: 0.8180 (mmt) REVERT: o 524 MET cc_start: 0.9044 (mpp) cc_final: 0.8582 (mpp) REVERT: o 637 MET cc_start: 0.9059 (ppp) cc_final: 0.8827 (ppp) REVERT: o 872 MET cc_start: 0.7888 (ptm) cc_final: 0.7446 (ptp) REVERT: o 1202 PHE cc_start: 0.5366 (t80) cc_final: 0.5025 (t80) REVERT: o 1228 MET cc_start: 0.5784 (ptt) cc_final: 0.5238 (ptt) REVERT: p 109 MET cc_start: 0.8402 (mpp) cc_final: 0.8050 (mpp) REVERT: p 162 LEU cc_start: 0.8936 (pt) cc_final: 0.8697 (pp) REVERT: p 368 MET cc_start: 0.7751 (ttt) cc_final: 0.7488 (ppp) REVERT: p 728 MET cc_start: 0.8946 (tmm) cc_final: 0.8541 (tmm) REVERT: p 802 ASP cc_start: 0.8926 (m-30) cc_final: 0.8618 (m-30) REVERT: p 921 ILE cc_start: 0.8592 (mm) cc_final: 0.8382 (mm) REVERT: p 952 GLU cc_start: 0.9096 (pm20) cc_final: 0.8799 (pm20) REVERT: p 968 ASN cc_start: 0.9036 (t0) cc_final: 0.8830 (t0) REVERT: p 1125 MET cc_start: 0.8372 (ppp) cc_final: 0.7789 (mmt) REVERT: p 1163 MET cc_start: 0.7549 (mmt) cc_final: 0.7222 (mmt) REVERT: s 151 MET cc_start: 0.7122 (ptp) cc_final: 0.6198 (ptp) REVERT: s 177 ASP cc_start: 0.8626 (p0) cc_final: 0.8421 (p0) REVERT: v 112 LEU cc_start: 0.8702 (mt) cc_final: 0.8326 (mt) REVERT: y 113 GLN cc_start: 0.6729 (mm110) cc_final: 0.6522 (pm20) outliers start: 0 outliers final: 0 residues processed: 501 average time/residue: 0.7454 time to fit residues: 657.5527 Evaluate side-chains 406 residues out of total 8741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 406 time to evaluate : 7.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 977 random chunks: chunk 475 optimal weight: 0.0040 chunk 615 optimal weight: 2.9990 chunk 825 optimal weight: 0.9980 chunk 237 optimal weight: 10.0000 chunk 714 optimal weight: 1.9990 chunk 114 optimal weight: 30.0000 chunk 215 optimal weight: 8.9990 chunk 776 optimal weight: 8.9990 chunk 324 optimal weight: 6.9990 chunk 797 optimal weight: 2.9990 chunk 98 optimal weight: 9.9990 overall best weight: 1.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 802 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 ASN ** B 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 915 GLN ** E 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 15 GLN ** I 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 60 HIS ** I 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 166 GLN ** R 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 238 GLN ** e 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 423 ASN ** o 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 677 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 721 HIS ** o 809 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o1077 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o1422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o1457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 930 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 970 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p1094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.109054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.097018 restraints weight = 639969.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.095835 restraints weight = 783181.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.095078 restraints weight = 656114.844| |-----------------------------------------------------------------------------| r_work (final): 0.4051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5775 moved from start: 0.6108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 83750 Z= 0.181 Angle : 0.589 16.991 113898 Z= 0.299 Chirality : 0.042 0.264 12709 Planarity : 0.004 0.050 14167 Dihedral : 13.561 178.527 12402 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.95 % Favored : 94.96 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % Cis-general : 0.00 % Twisted Proline : 0.21 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.09), residues: 9695 helix: 0.94 (0.09), residues: 3850 sheet: -0.09 (0.14), residues: 1306 loop : -1.11 (0.09), residues: 4539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 612 HIS 0.008 0.001 HIS p 970 PHE 0.020 0.001 PHE q 184 TYR 0.019 0.001 TYR z 41 ARG 0.012 0.000 ARG c 11 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14927.83 seconds wall clock time: 266 minutes 56.46 seconds (16016.46 seconds total)